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Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis
Rodrigo A Gutiérrez, Laurence V Lejay, Alexis Dean, Francesca Chiaromonte, Dennis E Shasha, Gloria M Coruzzi
Genome Biol. 2007; 8(1): R7. Published online 2007 January 11. doi: 10.1186/gb-2007-8-1-r7
PMCID:
PMC1839130
Abstract Full Text PDF–619K Supplementary Material

Is Cited by the Following 38 Articles in this Archive:

Metabolic Profiling of a Mapping Population Exposes New Insights in the Regulation of Seed Metabolism and Seed, Fruit, and Plant Relations
David Toubiana, Yaniv Semel, Takayuki Tohge, Romina Beleggia, Luigi Cattivelli, Leah Rosental, Zoran Nikoloski, Dani Zamir, Alisdair R. Fernie, Aaron Fait
PLoS Genet. 2012 March; 8(3): e1002612. Published online 2012 March 29. doi: 10.1371/journal.pgen.1002612
PMCID:
PMC3315483
Abstract Full Text PDF–7.2M Supplementary Material
Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches
Atsushi Fukushima, Tomoko Nishizawa, Mariko Hayakumo, Shoko Hikosaka, Kazuki Saito, Eiji Goto, Miyako Kusano
Plant Physiol. 2012 April; 158(4): 1487–1502. Published online 2012 February 3. doi: 10.1104/pp.111.188367
PMCID:
PMC3343727
Abstract Full Text PDF–1.4M Supplementary Material
Genome-Wide Identification of MicroRNAs in Response to Low Nitrate Availability in Maize Leaves and Roots
Zhenhua Xu, Sihui Zhong, Xinhai Li, Wenxue Li, Steven J. Rothstein, Shihuang Zhang, Yongmei Bi, Chuanxiao Xie
PLoS One. 2011; 6(11): e28009. Published online 2011 November 23. doi: 10.1371/journal.pone.0028009
PMCID:
PMC3223196
Abstract Full Text PDF–747K Supplementary Material
Arabidopsis Roots and Shoots Show Distinct Temporal Adaptation Patterns toward Nitrogen Starvation
Anne Krapp, Richard Berthomé, Mathilde Orsel, Stéphanie Mercey-Boutet, Agnes Yu, Loren Castaings, Samira Elftieh, Hilary Major, Jean-Pierre Renou, Françoise Daniel-Vedele
Plant Physiol. 2011 November; 157(3): 1255–1282. Published online 2011 September 7. doi: 10.1104/pp.111.179838
PMCID:
PMC3252138
Free in PMC on 2012/11/01
The Arabidopsis bZIP Gene AtbZIP63 Is a Sensitive Integrator of Transient Abscisic Acid and Glucose Signals
Cleverson Carlos Matiolli, Juarez Pires Tomaz, Gustavo Turqueto Duarte, Fernanda Manso Prado, Luiz Eduardo Vieira Del Bem, Amanda Bortolini Silveira, Luciane Gauer, Luiz Gustavo Guedes Corrêa, Rodrigo Duarte Drumond, Américo José Carvalho Viana, Paolo Di Mascio, Christian Meyer, Michel Vincentz
Plant Physiol. 2011 October; 157(2): 692–705. Published online 2011 August 15. doi: 10.1104/pp.111.181743
PMCID:
PMC3192551
Abstract Full Text PDF–946K
Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate
Gabriel Krouk, Piotr Mirowski, Yann LeCun, Dennis E Shasha, Gloria M Coruzzi
Genome Biol. 2010; 11(12): R123. Published online 2010 December 23. doi: 10.1186/gb-2010-11-12-r123
PMCID:
PMC3046483
Abstract Full Text PDF–2.1M Supplementary Material
Network news: prime time for systems biology of the plant circadian clock truncated form of the title: Plant circadian clocks
C. Robertson McClung, Rodrigo A. Gutiérrez
Curr Opin Genet Dev. Author manuscript; available in PMC 2011 December 1.
Published in final edited form as: Curr Opin Genet Dev. 2010 December; 20(6): 588–598. doi: 10.1016/j.gde.2010.08.010
PMCID:
PMC3098449
Abstract Full Text PDF–493K
Nitrate regulates floral induction in Arabidopsis, acting independently of light, gibberellin and autonomous pathways
Inmaculada Castro Marín, Irene Loef, Linda Bartetzko, Iain Searle, George Coupland, Mark Stitt, Daniel Osuna
Planta. 2011 March; 233(3): 539–552. Published online 2010 November 27. doi: 10.1007/s00425-010-1316-5
PMCID:
PMC3043248
Abstract Full Text PDF–968K Supplementary Material
Gene networks for N-sensing, signaling and response in Arabidopsis thaliana
Elena A Vidal, Karem P Tamayo, Rodrigo A Gutierrez
Wiley Interdiscip Rev Syst Biol Med. Author manuscript; available in PMC 2011 November 1.
Published in final edited form as: Wiley Interdiscip Rev Syst Biol Med. 2010 Nov-Dec; 2(6): 683–693. doi: 10.1002/wsbm.87
PMCID:
PMC2951390
Abstract Full Text PDF–88K
Digital Gene Expression Signatures for Maize Development
Andrea L. Eveland, Namiko Satoh-Nagasawa, Alexander Goldshmidt, Sandra Meyer, Mary Beatty, Hajime Sakai, Doreen Ware, David Jackson
Plant Physiol. 2010 November; 154(3): 1024–1039. Published online 2010 September 10. doi: 10.1104/pp.110.159673
PMCID:
PMC2971585
Abstract Full Text PDF–1005K Supplementary Material
Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis
Mariana Obertello, Gabriel Krouk, Manpreet S Katari, Suzan J Runko, Gloria M Coruzzi
BMC Syst Biol. 2010; 4: 111. Published online 2010 August 12. doi: 10.1186/1752-0509-4-111
PMCID:
PMC2933594
Abstract Full Text PDF–757K Supplementary Material
Identification of Arabidopsis Mutants Impaired in the Systemic Regulation of Root Nitrate Uptake by the Nitrogen Status of the Plant
Thomas Girin, El-Sayed El-Kafafi, Thomas Widiez, Alexander Erban, Hans-Michael Hubberten, Joachim Kopka, Rainer Hoefgen, Alain Gojon, Marc Lepetit
Plant Physiol. 2010 July; 153(3): 1250–1260. Published online 2010 May 6. doi: 10.1104/pp.110.157354
PMCID:
PMC2899898
Abstract Full Text PDF–615K Supplementary Material
Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution
Angélica Cibrián-Jaramillo, Jose E. De la Torre-Bárcena, Ernest K. Lee, Manpreet S. Katari, Damon P. Little, Dennis W. Stevenson, Rob Martienssen, Gloria M. Coruzzi, Rob DeSalle
Genome Biol Evol. 2010; 2: 225–239. Published online 2010 March 24. doi: 10.1093/gbe/evq012
PMCID:
PMC2997538
Abstract Full Text PDF–1.4M
Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana
Elena A. Vidal, Viviana Araus, Cheng Lu, Geraint Parry, Pamela J. Green, Gloria M. Coruzzi, Rodrigo A. Gutiérrez
Proc Natl Acad Sci U S A. 2010 March 2; 107(9): 4477–4482. Published online 2010 February 8. doi: 10.1073/pnas.0909571107
PMCID:
PMC2840086
Abstract Full Text PDF–438K Supplementary Material
VirtualPlant: A Software Platform to Support Systems Biology Research
Manpreet S. Katari, Steve D. Nowicki, Felipe F. Aceituno, Damion Nero, Jonathan Kelfer, Lee Parnell Thompson, Juan M. Cabello, Rebecca S. Davidson, Arthur P. Goldberg, Dennis E. Shasha, Gloria M. Coruzzi, Rodrigo A. Gutiérrez
Plant Physiol. 2010 February; 152(2): 500–515. doi: 10.1104/pp.109.147025
PMCID:
PMC2815851
Abstract Full Text PDF–2.2M Supplementary Material
A Systems View of Responses to Nutritional Cues in Arabidopsis: Toward a Paradigm Shift for Predictive Network Modeling
Sandrine Ruffel, Gabriel Krouk, Gloria M. Coruzzi
Plant Physiol. 2010 February; 152(2): 445–452. doi: 10.1104/pp.109.148502
PMCID:
PMC2815908
Full Text PDF–243K
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
Insuk Lee, Bindu Ambaru, Pranjali Thakkar, Edward M. Marcotte, Seung Y. Rhee
Nat Biotechnol. Author manuscript; available in PMC 2010 April 20.
Published in final edited form as: Nat Biotechnol. 2010 February; 28(2): 149–156. Published online 2010 January 31. doi: 10.1038/nbt.1603
PMCID:
PMC2857375
Abstract Full Text PDF–2.5M Supplementary Material
CORNET: A User-Friendly Tool for Data Mining and Integration
Stefanie De Bodt, Diana Carvajal, Jens Hollunder, Joost Van den Cruyce, Sara Movahedi, Dirk Inzé
Plant Physiol. 2010 March; 152(3): 1167–1179. Published online 2010 January 6. doi: 10.1104/pp.109.147215
PMCID:
PMC2832254
Abstract Full Text PDF–1.4M Supplementary Material
Arabidopsis N-MYC DOWNREGULATED-LIKE1, a Positive Regulator of Auxin Transport in a G Protein–Mediated Pathway
Yashwanti Mudgil, Joachm F. Uhrig, Jiping Zhou, Brenda Temple, Kun Jiang, Alan M. Jones
Plant Cell. 2009 November; 21(11): 3591–3609. doi: 10.1105/tpc.109.065557
PMCID:
PMC2798320
Abstract Full Text PDF–1.9M Supplementary Material
A Genetic Screen for Nitrate Regulatory Mutants Captures the Nitrate Transporter Gene NRT1.1
Rongchen Wang, Xiujuan Xing, Yong Wang, Amy Tran, Nigel M. Crawford
Plant Physiol. 2009 September; 151(1): 472–478. doi: 10.1104/pp.109.140434
PMCID:
PMC2735993
Abstract Full Text PDF–245K Supplementary Material
A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule"
Damion Nero, Gabriel Krouk, Daniel Tranchina, Gloria M Coruzzi
BMC Syst Biol. 2009; 3: 59. Published online 2009 June 6. doi: 10.1186/1752-0509-3-59
PMCID:
PMC2702358
Abstract Full Text PDF–1.4M Supplementary Material
Arabidopsis thaliana as a Model Organism in Systems Biology
Jaimie M. Van Norman, Philip N. Benfey
Wiley Interdiscip Rev Syst Biol Med. Author manuscript; available in PMC 2010 April 29.
Published in final edited form as: Wiley Interdiscip Rev Syst Biol Med. 2009 April 29; 1(3): 372–379. doi: 10.1002/wsbm.25
PMCID:
PMC2836806
Abstract Full Text PDF–536K Supplementary Material
Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology
Siobhan M. Brady, Nicholas J. Provart
Plant Cell. 2009 April; 21(4): 1034–1051. doi: 10.1105/tpc.109.066050
PMCID:
PMC2685637
Abstract Full Text PDF–887K
A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis
Gabriel Krouk, Daniel Tranchina, Laurence Lejay, Alexis A. Cruikshank, Dennis Shasha, Gloria M. Coruzzi, Rodrigo A. Gutiérrez
PLoS Comput Biol. 2009 March; 5(3): e1000326. Published online 2009 March 20. doi: 10.1371/journal.pcbi.1000326
PMCID:
PMC2652106
Abstract Full Text PDF–720K 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 Carbon and Nitrogen Metabolism with Energy Production Is Crucial to Light Acclimation in the Cyanobacterium Synechocystis
Abhay K. Singh, Thanura Elvitigala, Maitrayee Bhattacharyya-Pakrasi, Rajeev Aurora, Bijoy Ghosh, Himadri B. Pakrasi
Plant Physiol. 2008 September; 148(1): 467–478. doi: 10.1104/pp.108.123489
PMCID:
PMC2528105
Abstract Full Text PDF–823K Supplementary Material
Arabidopsis Reactome: A Foundation Knowledgebase for Plant Systems Biology
Nicolas Tsesmetzis, Matthew Couchman, Janet Higgins, Alison Smith, John H. Doonan, Georg J. Seifert, Esther E. Schmidt, Imre Vastrik, Ewan Birney, Guanming Wu, Peter D'Eustachio, Lincoln D. Stein, Richard J. Morris, Michael W. Bevan, Sean V. Walsh
Plant Cell. 2008 June; 20(6): 1426–1436. doi: 10.1105/tpc.108.057976
PMCID:
PMC2483364
Full Text PDF–1.5M Supplementary Material
Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis
Kevin Horan, Charles Jang, Julia Bailey-Serres, Ron Mittler, Christian Shelton, Jeff F. Harper, Jian-Kang Zhu, John C. Cushman, Martin Gollery, Thomas Girke
Plant Physiol. 2008 May; 147(1): 41–57. doi: 10.1104/pp.108.117366
PMCID:
PMC2330292
Abstract Full Text PDF–837K Supplementary Material
Regulating the Regulators: The Future Prospects for Transcription-Factor-Based Agricultural Biotechnology Products
Karen Century, T. Lynne Reuber, Oliver J. Ratcliffe
Plant Physiol. 2008 May; 147(1): 20–29. doi: 10.1104/pp.108.117887
PMCID:
PMC2330319
Full Text PDF–137K
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis
Karen E Thum, Michael J Shin, Rodrigo A Gutiérrez, Indrani Mukherjee, Manpreet S Katari, Damion Nero, Dennis Shasha, Gloria M Coruzzi
BMC Syst Biol. 2008; 2: 31. Published online 2008 April 4. doi: 10.1186/1752-0509-2-31
PMCID:
PMC2335094
Abstract Full Text PDF–1.2M Supplementary Material
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