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Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes
Yves Gibon, Bjoern Usadel, Oliver E Blaesing, Beate Kamlage, Melanie Hoehne, Richard Trethewey, Mark Stitt
Genome Biol. 2006; 7(8): R76. Published online 2006 August 17. doi: 10.1186/gb-2006-7-8-r76
PMCID:
PMC1779593
Abstract Full Text PDF–917K Supplementary Material
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 Is Cited by the Following 34 Articles in this Archive:
Tissue Specific Diurnal Rhythms of Metabolites and Their Regulation during Herbivore Attack in a Native Tobacco, Nicotiana attenuata
Sang-Gyu Kim, Felipe Yon, Emmanuel Gaquerel, Jyotasana Gulati, Ian T. Baldwin
PLoS One. 2011; 6(10): e26214. Published online 2011 October 18. doi: 10.1371/journal.pone.0026214
PMCID:
PMC3196511
Abstract Full Text PDF–2.4M Supplementary Material
Label-free shotgun proteomics and metabolite analysis reveal a significant metabolic shift during citrus fruit development
Ehud Katz, Kyung Hwan Boo, Ho Youn Kim, Richard A. Eigenheer, Brett S. Phinney, Vladimir Shulaev, Florence Negre-Zakharov, Avi Sadka, Eduardo Blumwald
J Exp Bot. 2011 November; 62(15): 5367–5384. Published online 2011 August 12. doi: 10.1093/jxb/err197
PMCID:
PMC3223037
Abstract Full Text PDF–1004K Supplementary Material
Detection and interpretation of metabolite–transcript coresponses using combined profiling data
Henning Redestig, Ivan G. Costa
Bioinformatics. 2011 July 1; 27(13): i357–i365. Published online 2011 June 14. doi: 10.1093/bioinformatics/btr231
PMCID:
PMC3117345
Abstract Full Text Supplementary Material
Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells
Rachel Cavill, Atanas Kamburov, James K. Ellis, Toby J. Athersuch, Marcus S. C. Blagrove, Ralf Herwig, Timothy M. D. Ebbels, Hector C. Keun
PLoS Comput Biol. 2011 March; 7(3): e1001113. Published online 2011 March 31. doi: 10.1371/journal.pcbi.1001113
PMCID:
PMC3068923
Abstract Full Text PDF–2.1M Supplementary Material
Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves
Wenying Xu, Rendong Yang, Meina Li, Zhuo Xing, Wenqiang Yang, Guang Chen, Han Guo, Xiaojie Gong, Zhou Du, Zhenhai Zhang, Xingming Hu, Dong Wang, Qian Qian, Tai Wang, Zhen Su, Yongbiao Xue
PLoS One. 2011; 6(3): e17613. Published online 2011 March 2. doi: 10.1371/journal.pone.0017613
PMCID:
PMC3047585
Abstract Full Text PDF–1.2M Supplementary Material
Interaction with Diurnal and Circadian Regulation Results in Dynamic Metabolic and Transcriptional Changes during Cold Acclimation in Arabidopsis
Carmen Espinoza, Thomas Degenkolbe, Camila Caldana, Ellen Zuther, Andrea Leisse, Lothar Willmitzer, Dirk K. Hincha, Matthew A. Hannah
PLoS One. 2010; 5(11): e14101. Published online 2010 November 23. doi: 10.1371/journal.pone.0014101
PMCID:
PMC2990718
Abstract Full Text PDF–2.1M Supplementary Material
A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana
Max Sajitz-Hermstein, Zoran Nikoloski
Bioinformatics. 2010 September 15; 26(18): i582–i588. Published online 2010 September 4. doi: 10.1093/bioinformatics/btq390
PMCID:
PMC2935400
Abstract Full Text PDF–201K Supplementary Material
Network Analysis of Enzyme Activities and Metabolite Levels and Their Relationship to Biomass in a Large Panel of Arabidopsis Accessions
Ronan Sulpice, Sandra Trenkamp, Matthias Steinfath, Bjorn Usadel, Yves Gibon, Hanna Witucka-Wall, Eva-Theresa Pyl, Hendrik Tschoep, Marie Caroline Steinhauser, Manuela Guenther, Melanie Hoehne, Johann M. Rohwer, Thomas Altmann, Alisdair R. Fernie, Mark Stitt
Plant Cell. 2010 August; 22(8): 2872–2893. Published online 2010 August 10. doi: 10.1105/tpc.110.076653
PMCID:
PMC2947169
Abstract Full Text PDF–1.3M Supplementary Material
Arabidopsis Plants Acclimate to Water Deficit at Low Cost through Changes of Carbon Usage: An Integrated Perspective Using Growth, Metabolite, Enzyme, and Gene Expression Analysis
Irène Hummel, Florent Pantin, Ronan Sulpice, Maria Piques, Gaëlle Rolland, Myriam Dauzat, Angélique Christophe, Marjorie Pervent, Marie Bouteillé, Mark Stitt, Yves Gibon, Bertrand Muller
Plant Physiol. 2010 September; 154(1): 357–372. Published online 2010 July 14. doi: 10.1104/pp.110.157008
PMCID:
PMC2938159
Abstract Full Text PDF–1.2M Supplementary Material
Diurnal Changes in Mitochondrial Function Reveal Daily Optimization of Light and Dark Respiratory Metabolism in Arabidopsis
Chun Pong Lee, Holger Eubel, A. Harvey Millar
Mol Cell Proteomics. 2010 October; 9(10): 2125–2139. Published online 2010 July 2. doi: 10.1074/mcp.M110.001214
PMCID:
PMC2953910
Abstract Full Text Supplementary Material
Enhancement of Plant Metabolite Fingerprinting by Machine Learning
Ian M. Scott, Cornelia P. Vermeer, Maria Liakata, Delia I. Corol, Jane L. Ward, Wanchang Lin, Helen E. Johnson, Lynne Whitehead, Baldeep Kular, John M. Baker, Sean Walsh, Anuja Dave, Tony R. Larson, Ian A. Graham, Trevor L. Wang, Ross D. King, John Draper, Michael H. Beale
Plant Physiol. 2010 August; 153(4): 1506–1520. Published online 2010 June 21. doi: 10.1104/pp.109.150524
PMCID:
PMC2923910
Abstract Full Text PDF–879K Supplementary Material
Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis
Elizabeth Allen, Annick Moing, Timothy MD Ebbels, Mickaël Maucourt, A Deri Tomos, Dominique Rolin, Mark A Hooks
BMC Syst Biol. 2010; 4: 62. Published online 2010 May 13. doi: 10.1186/1752-0509-4-62
PMCID:
PMC2890501
Abstract Full Text PDF–1.3M Supplementary Material
Increased Leaf Size: Different Means to an End
Nathalie Gonzalez, Stefanie De Bodt, Ronan Sulpice, Yusuke Jikumaru, Eunyoung Chae, Stijn Dhondt, Twiggy Van Daele, Liesbeth De Milde, Detlef Weigel, Yuji Kamiya, Mark Stitt, Gerrit T.S. Beemster, Dirk Inzé
Plant Physiol. 2010 July; 153(3): 1261–1279. Published online 2010 May 11. doi: 10.1104/pp.110.156018
PMCID:
PMC2899902
Abstract Full Text PDF–1.4M Supplementary Material
Probing the Reproducibility of Leaf Growth and Molecular Phenotypes: A Comparison of Three Arabidopsis Accessions Cultivated in Ten Laboratories
Catherine Massonnet, Denis Vile, Juliette Fabre, Matthew A. Hannah, Camila Caldana, Jan Lisec, Gerrit T.S. Beemster, Rhonda C. Meyer, Gaëlle Messerli, Jesper T. Gronlund, Josip Perkovic, Emma Wigmore, Sean May, Michael W. Bevan, Christian Meyer, Silvia Rubio-Díaz, Detlef Weigel, José Luis Micol, Vicky Buchanan-Wollaston, Fabio Fiorani, Sean Walsh, Bernd Rinn, Wilhelm Gruissem, Pierre Hilson, Lars Hennig, Lothar Willmitzer, Christine Granier
Plant Physiol. 2010 April; 152(4): 2142–2157. Published online 2010 March 3. doi: 10.1104/pp.109.148338
PMCID:
PMC2850010
Abstract Full Text PDF–747K Supplementary Material
Combined Transcript and Metabolite Profiling of Arabidopsis Grown under Widely Variant Growth Conditions Facilitates the Identification of Novel Metabolite-Mediated Regulation of Gene Expression
Matthew A. Hannah, Camila Caldana, Dirk Steinhauser, Ilse Balbo, Alisdair R. Fernie, Lothar Willmitzer
Plant Physiol. 2010 April; 152(4): 2120–2129. Published online 2010 February 26. doi: 10.1104/pp.109.147306
PMCID:
PMC2850026
Abstract Full Text PDF–701K Supplementary Material
Metabolic Networks: How to Identify Key Components in the Regulation of Metabolism and Growth
Mark Stitt, Ronan Sulpice, Joost Keurentjes
Plant Physiol. 2010 February; 152(2): 428–444. doi: 10.1104/pp.109.150821
PMCID:
PMC2815907
Full Text PDF–200K
Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis
Maria Piques, Waltraud X Schulze, Melanie Höhne, Björn Usadel, Yves Gibon, Johann Rohwer, Mark Stitt
Mol Syst Biol. 2009; 5: 314. Published online 2009 October 13. doi: 10.1038/msb.2009.68
PMCID:
PMC2779082
Abstract Full Text PDF–1.8M Supplementary Material
Dynamic Plastid Redox Signals Integrate Gene Expression and Metabolism to Induce Distinct Metabolic States in Photosynthetic Acclimation in Arabidopsis
Katharina Bräutigam, Lars Dietzel, Tatjana Kleine, Elke Ströher, Dennis Wormuth, Karl-Josef Dietz, Dörte Radke, Markus Wirtz, Rüdiger Hell, Peter Dörmann, Adriano Nunes-Nesi, Nicolas Schauer, Alisdair R. Fernie, Sandra N. Oliver, Peter Geigenberger, Dario Leister, Thomas Pfannschmidt
Plant Cell. 2009 September; 21(9): 2715–2732. doi: 10.1105/tpc.108.062018
PMCID:
PMC2768923
Abstract Full Text PDF–1.3M Supplementary Material
Metabolic responses to salt stress of barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differ in salinity tolerance
Widodo, John H. Patterson, Ed Newbigin, Mark Tester, Antony Bacic, Ute Roessner
J Exp Bot. 2009 October; 60(14): 4089–4103. Published online 2009 August 10. doi: 10.1093/jxb/erp243
PMCID:
PMC2755029
Abstract Full Text PDF–546K Supplementary Material
Sucrose Control of Translation Mediated by an Upstream Open Reading Frame-Encoded Peptide
Fatemeh Rahmani, Maureen Hummel, Jolanda Schuurmans, Anika Wiese-Klinkenberg, Sjef Smeekens, Johannes Hanson
Plant Physiol. 2009 July; 150(3): 1356–1367. doi: 10.1104/pp.109.136036
PMCID:
PMC2705056
Abstract Full Text PDF–848K Supplementary Material
Regulatory Features Underlying Pollination-Dependent and -Independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling
Hua Wang, Nicolas Schauer, Bjoern Usadel, Pierre Frasse, Mohamed Zouine, Michel Hernould, Alain Latché, Jean-Claude Pech, Alisdair R. Fernie, Mondher Bouzayen
Plant Cell. 2009 May; 21(5): 1428–1452. doi: 10.1105/tpc.108.060830
PMCID:
PMC2700536
Abstract Full Text PDF–3.2M Supplementary Material
Application of GC-MS for the detection of lipophilic compounds in diverse plant tissues
Anna Lytovchenko, Romina Beleggia, Nicolas Schauer, Tal Isaacson, Jan E Leuendorf, Hanjo Hellmann, Jocelyn KC Rose, Alisdair R Fernie
Plant Methods. 2009; 5: 4. Published online 2009 April 24. doi: 10.1186/1746-4811-5-4
PMCID:
PMC2680844
Abstract Full Text PDF–312K Supplementary Material
Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination
Atsushi Fukushima, Miyako Kusano, Norihito Nakamichi, Makoto Kobayashi, Naomi Hayashi, Hitoshi Sakakibara, Takeshi Mizuno, Kazuki Saito
Proc Natl Acad Sci U S A. 2009 April 28; 106(17): 7251–7256. Published online 2009 April 9. doi: 10.1073/pnas.0900952106
Correction in:
Proc Natl Acad Sci U S A. 2009 May 26; 106(21): 8791.
PMCID:
PMC2667372
Abstract Full Text PDF–1.2M Supplementary Material Correction
Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae
Patrick H. Bradley, Matthew J. Brauer, Joshua D. Rabinowitz, Olga G. Troyanskaya
PLoS Comput Biol. 2009 January; 5(1): e1000270. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000270
PMCID:
PMC2614473
Abstract Full Text PDF–496K Supplementary Material
Sugar Sensing and Signaling
Matthew Ramon, Filip Rolland, Jen Sheen
Arabidopsis Book. 2008; 6: e0117. Published online 2008 October 22. doi: 10.1199/tab.0117
PMCID:
PMC3243355
Abstract Full Text PDF–451K
Integration of Metabolomic and Proteomic Phenotypes: Analysis of Data Covariance Dissects Starch and RFO Metabolism from Low and High Temperature Compensation Response in Arabidopsis Thaliana
Stefanie Wienkoop, Katja Morgenthal, Florian Wolschin, Matthias Scholz, Joachim Selbig, Wolfram Weckwerth
Mol Cell Proteomics. 2008 September; 7(9): 1725–1736. doi: 10.1074/mcp.M700273-MCP200
PMCID:
PMC2556022
Abstract Full Text Supplementary Material
Integrative analyses of genetic variation in enzyme activities of primary carbohydrate metabolism reveal distinct modes of regulation in Arabidopsis thaliana
Joost JB Keurentjes, Ronan Sulpice, Yves Gibon, Marie-Caroline Steinhauser, Jingyuan Fu, Maarten Koornneef, Mark Stitt, Dick Vreugdenhil
Genome Biol. 2008; 9(8): R129. Published online 2008 August 18. doi: 10.1186/gb-2008-9-8-r129
PMCID:
PMC2575519
Abstract Full Text PDF–638K Supplementary Material
If the antibody fails – a mass Western approach
Ute Lehmann, Stefanie Wienkoop, Hendrik Tschoep, Wolfram Weckwerth
Plant J. 2008 September; 55(6): 1039–1046. Published online 2008 July 9. doi: 10.1111/j.1365-313X.2008.03554.x
PMCID:
PMC2607522
Abstract Full Text PDF–279K
Mild Reductions in Mitochondrial Citrate Synthase Activity Result in a Compromised Nitrate Assimilation and Reduced Leaf Pigmentation But Have No Effect on Photosynthetic Performance or Growth
Agata Sienkiewicz-Porzucek, Adriano Nunes-Nesi, Ronan Sulpice, Jan Lisec, Danilo C. Centeno, Petronia Carillo, Andrea Leisse, Ewa Urbanczyk-Wochniak, Alisdair R. Fernie
Plant Physiol. 2008 May; 147(1): 115–127. doi: 10.1104/pp.108.117978
PMCID:
PMC2330314
Abstract Full Text PDF–989K Supplementary Material
Global Transcript Levels Respond to Small Changes of the Carbon Status during Progressive Exhaustion of Carbohydrates in Arabidopsis Rosettes
Björn Usadel, Oliver E. Bläsing, Yves Gibon, Kristin Retzlaff, Melanie Höhne, Manuela Günther, Mark Stitt
Plant Physiol. 2008 April; 146(4): 1834–1861. doi: 10.1104/pp.107.115592
PMCID:
PMC2287354
Abstract Full Text PDF–3.4M Supplementary Material
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