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Swift, J, Greenham, K, Ecker, JR, Coruzzi, GM, Robertson McClung, C. The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues. Plant J. 2022;109 (4):764-778. doi: 10.1111/tpj.15589. PubMed PMID:34797944 PubMed Central PMC9215356.

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Cheng, CY, Li, Y, Varala, K, Bubert, J, Huang, J, Kim, GJ et al.. Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships. Nat Commun. 2021;12 (1):5627. doi: 10.1038/s41467-021-25893-w. PubMed PMID:34561450 PubMed Central PMC8463701.

Safi, A, Medici, A, Szponarski, W, Martin, F, Clément-Vidal, A, Marshall-Colon, A et al.. GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways. J Exp Bot. 2021;72 (10):3881-3901. doi: 10.1093/jxb/erab114. PubMed PMID:33758916 PubMed Central PMC8096604.

Alvarez, JM, Brooks, MD, Swift, J, Coruzzi, GM. Time-Based Systems Biology Approaches to Capture and Model Dynamic Gene Regulatory Networks. Annu Rev Plant Biol. 2021;72 :105-131. doi: 10.1146/annurev-arplant-081320-090914. PubMed PMID:33667112 PubMed Central PMC9312366.

Brooks, MD, Juang, CL, Katari, MS, Alvarez, JM, Pasquino, A, Shih, HJ et al.. ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks. Plant Physiol. 2021;185 (1):49-66. doi: 10.1093/plphys/kiaa012. PubMed PMID:33631799 PubMed Central PMC8133578.

Cirrone, J, Brooks, MD, Bonneau, R, Coruzzi, GM, Shasha, DE. Author Correction: OutPredict: multiple datasets can improve prediction of expression and inference of causality. Sci Rep. 2020;10 (1):14141. doi: 10.1038/s41598-020-69883-2. PubMed PMID:32811842 PubMed Central PMC7435169.

Swift, J, Alvarez, JM, Araus, V, Gutiérrez, RA, Coruzzi, GM. Nutrient dose-responsive transcriptome changes driven by Michaelis-Menten kinetics underlie plant growth rates. Proc Natl Acad Sci U S A. 2020;117 (23):12531-12540. doi: 10.1073/pnas.1918619117. PubMed PMID:32414922 PubMed Central PMC7293603.

Cirrone, J, Brooks, MD, Bonneau, R, Coruzzi, GM, Shasha, DE. OutPredict: multiple datasets can improve prediction of expression and inference of causality. Sci Rep. 2020;10 (1):6804. doi: 10.1038/s41598-020-63347-3. PubMed PMID:32321967 PubMed Central PMC7176633.

Zhang, X, Ménard, R, Li, Y, Coruzzi, GM, Heitz, T, Shen, WH et al.. Arabidopsis SDG8 Potentiates the Sustainable Transcriptional Induction of the Pathogenesis-Related Genes PR1 and PR2 During Plant Defense Response. Front Plant Sci. 2020;11 :277. doi: 10.3389/fpls.2020.00277. PubMed PMID:32218796 PubMed Central PMC7078350.

Vidal, EA, Alvarez, JM, Araus, V, Riveras, E, Brooks, MD, Krouk, G et al.. Nitrate in 2020: Thirty Years from Transport to Signaling Networks. Plant Cell. 2020;32 (7):2094-2119. doi: 10.1105/tpc.19.00748. PubMed PMID:32169959 PubMed Central PMC7346567.

Alvarez, JM, Schinke, AL, Brooks, MD, Pasquino, A, Leonelli, L, Varala, K et al.. Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade. Nat Commun. 2020;11 (1):1157. doi: 10.1038/s41467-020-14979-6. PubMed PMID:32123177 PubMed Central PMC7052136.

Araus, V, Swift, J, Alvarez, JM, Henry, A, Coruzzi, GM. A balancing act: how plants integrate nitrogen and water signals. J Exp Bot. 2020;71 (15):4442-4451. doi: 10.1093/jxb/eraa054. PubMed PMID:31990028 PubMed Central PMC7382378.

Li, Y, Brooks, M, Yeoh-Wang, J, McCoy, RM, Rock, TM, Pasquino, A et al.. SDG8-Mediated Histone Methylation and RNA Processing Function in the Response to Nitrate Signaling. Plant Physiol. 2020;182 (1):215-227. doi: 10.1104/pp.19.00682. PubMed PMID:31641075 PubMed Central PMC6945839.

Heerah, S, Katari, M, Penjor, R, Coruzzi, G, Marshall-Colon, A. WRKY1 Mediates Transcriptional Regulation of Light and Nitrogen Signaling Pathways. Plant Physiol. 2019;181 (3):1371-1388. doi: 10.1104/pp.19.00685. PubMed PMID:31409699 PubMed Central PMC6836853.

Falter-Braun, P, Brady, S, Gutiérrez, RA, Coruzzi, GM, Krouk, G. iPlant Systems Biology (iPSB): An International Network Hub in the Plant Community. Mol Plant. 2019;12 (6):727-730. doi: 10.1016/j.molp.2019.05.005. PubMed PMID:31125688 .

Brooks, MD, Cirrone, J, Pasquino, AV, Alvarez, JM, Swift, J, Mittal, S et al.. Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions. Nat Commun. 2019;10 (1):1569. doi: 10.1038/s41467-019-09522-1. PubMed PMID:30952851 PubMed Central PMC6451032.

Swift, J, Adame, M, Tranchina, D, Henry, A, Coruzzi, GM. Water impacts nutrient dose responses genome-wide to affect crop production. Nat Commun. 2019;10 (1):1374. doi: 10.1038/s41467-019-09287-7. PubMed PMID:30914651 PubMed Central PMC6435674.

Varala, K, Marshall-Colón, A, Cirrone, J, Brooks, MD, Pasquino, AV, Léran, S et al.. Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. Proc Natl Acad Sci U S A. 2018;115 (25):6494-6499. doi: 10.1073/pnas.1721487115. PubMed PMID:29769331 PubMed Central PMC6016767.

Para, A, Li, Y, Coruzzi, GM. μChIP-Seq for Genome-Wide Mapping of In Vivo TF-DNA Interactions in Arabidopsis Root Protoplasts. Methods Mol Biol. 2018;1761 :249-261. doi: 10.1007/978-1-4939-7747-5_19. PubMed PMID:29525963 .

Walker, L, Boddington, C, Jenkins, D, Wang, Y, Grønlund, JT, Hulsmans, J et al.. Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture. Plant Cell. 2017;29 (10):2393-2412. doi: 10.1105/tpc.16.00961. PubMed PMID:28893852 PubMed Central PMC5774560.

Ristova, D, Carré, C, Pervent, M, Medici, A, Kim, GJ, Scalia, D et al.. Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root. Sci Signal. 2016;9 (451):rs13. doi: 10.1126/scisignal.aaf2768. PubMed PMID:27811143 .

Swift, J, Coruzzi, GM. A matter of time - How transient transcription factor interactions create dynamic gene regulatory networks. Biochim Biophys Acta Gene Regul Mech. 2017;1860 (1):75-83. doi: 10.1016/j.bbagrm.2016.08.007. PubMed PMID:27546191 PubMed Central PMC5203810.

O'Brien, JA, Vega, A, Bouguyon, E, Krouk, G, Gojon, A, Coruzzi, G et al.. Nitrate Transport, Sensing, and Responses in Plants. Mol Plant. 2016;9 (6):837-56. doi: 10.1016/j.molp.2016.05.004. PubMed PMID:27212387 .

Doidy, J, Li, Y, Neymotin, B, Edwards, MB, Varala, K, Gresham, D et al.. "Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run". BMC Genomics. 2016;17 :92. doi: 10.1186/s12864-016-2410-2. PubMed PMID:26843062 PubMed Central PMC4738784.

Ruffel, S, Poitout, A, Krouk, G, Coruzzi, GM, Lacombe, B. Long-distance nitrate signaling displays cytokinin dependent and independent branches. J Integr Plant Biol. 2016;58 (3):226-9. doi: 10.1111/jipb.12453. PubMed PMID:26619818 .

Varala, K, Li, Y, Marshall-Colón, A, Para, A, Coruzzi, GM. "Hit-and-Run" leaves its mark: catalyst transcription factors and chromatin modification. Bioessays. 2015;37 (8):851-6. doi: 10.1002/bies.201400205. PubMed PMID:26108710 PubMed Central PMC4548861.

Li, Y, Varala, K, Coruzzi, GM. From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks. Trends Genet. 2015;31 (9):509-15. doi: 10.1016/j.tig.2015.05.005. PubMed PMID:26072453 PubMed Central PMC4558309.

Obertello, M, Shrivastava, S, Katari, MS, Coruzzi, GM. Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice. Plant Physiol. 2015;168 (4):1830-43. doi: 10.1104/pp.114.255877. PubMed PMID:26045464 PubMed Central PMC4528727.

Li, Y, Mukherjee, I, Thum, KE, Tanurdzic, M, Katari, MS, Obertello, M et al.. The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants. Genome Biol. 2015;16 (1):79. doi: 10.1186/s13059-015-0640-2. PubMed PMID:25928034 PubMed Central PMC4464704.

Medici, A, Marshall-Colon, A, Ronzier, E, Szponarski, W, Wang, R, Gojon, A et al.. AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip. Nat Commun. 2015;6 :6274. doi: 10.1038/ncomms7274. PubMed PMID:25723764 PubMed Central PMC4373655.

Delaux, PM, Varala, K, Edger, PP, Coruzzi, GM, Pires, JC, Ané, JM et al.. Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution. PLoS Genet. 2014;10 (7):e1004487. doi: 10.1371/journal.pgen.1004487. PubMed PMID:25032823 PubMed Central PMC4102449.

Li, Y, Krouk, G, Coruzzi, GM, Ruffel, S. Finding a nitrogen niche: a systems integration of local and systemic nitrogen signalling in plants. J Exp Bot. 2014;65 (19):5601-10. doi: 10.1093/jxb/eru263. PubMed PMID:24963003 .

Para, A, Li, Y, Marshall-Colón, A, Varala, K, Francoeur, NJ, Moran, TM et al.. Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. Proc Natl Acad Sci U S A. 2014;111 (28):10371-6. doi: 10.1073/pnas.1404657111. PubMed PMID:24958886 PubMed Central PMC4104873.

Vidal, EA, Moyano, TC, Krouk, G, Katari, MS, Tanurdzic, M, McCombie, WR et al.. Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics. 2013;14 :701. doi: 10.1186/1471-2164-14-701. PubMed PMID:24119003 PubMed Central PMC3906980.

Léran, S, Varala, K, Boyer, JC, Chiurazzi, M, Crawford, N, Daniel-Vedele, F et al.. A unified nomenclature of NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family members in plants. Trends Plant Sci. 2014;19 (1):5-9. doi: 10.1016/j.tplants.2013.08.008. PubMed PMID:24055139 .

Gifford, ML, Banta, JA, Katari, MS, Hulsmans, J, Chen, L, Ristova, D et al.. Plasticity regulators modulate specific root traits in discrete nitrogen environments. PLoS Genet. 2013;9 (9):e1003760. doi: 10.1371/journal.pgen.1003760. PubMed PMID:24039603 PubMed Central PMC3764102.

Rosas, U, Cibrian-Jaramillo, A, Ristova, D, Banta, JA, Gifford, ML, Fan, AH et al.. Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture. Proc Natl Acad Sci U S A. 2013;110 (37):15133-8. doi: 10.1073/pnas.1305883110. PubMed PMID:23980140 PubMed Central PMC3773737.

Krouk, G, Lingeman, J, Colon, AM, Coruzzi, G, Shasha, D. Gene regulatory networks in plants: learning causality from time and perturbation. Genome Biol. 2013;14 (6):123. doi: 10.1186/gb-2013-14-6-123. PubMed PMID:23805876 PubMed Central PMC3707030.

Bargmann, BO, Marshall-Colon, A, Efroni, I, Ruffel, S, Birnbaum, KD, Coruzzi, GM et al.. TARGET: a transient transformation system for genome-wide transcription factor target discovery. Mol Plant. 2013;6 (3):978-80. doi: 10.1093/mp/sst010. PubMed PMID:23335732 PubMed Central PMC3660954.

Ristova, D, Rosas, U, Krouk, G, Ruffel, S, Birnbaum, KD, Coruzzi, GM et al.. RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis. Plant Physiol. 2013;161 (3):1086-96. doi: 10.1104/pp.112.210872. PubMed PMID:23335624 PubMed Central PMC3585581.

Lee, EK, Cibrian-Jaramillo, A, Kolokotronis, SO, Katari, MS, Stamatakis, A, Ott, M et al.. A functional phylogenomic view of the seed plants. PLoS Genet. 2011;7 (12):e1002411. doi: 10.1371/journal.pgen.1002411. PubMed PMID:22194700 PubMed Central PMC3240601.

Ruffel, S, Krouk, G, Ristova, D, Shasha, D, Birnbaum, KD, Coruzzi, GM et al.. Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand. Proc Natl Acad Sci U S A. 2011;108 (45):18524-9. doi: 10.1073/pnas.1108684108. PubMed PMID:22025711 PubMed Central PMC3215050.

Widiez, T, El Kafafi, el S, Girin, T, Berr, A, Ruffel, S, Krouk, G et al.. High nitrogen insensitive 9 (HNI9)-mediated systemic repression of root NO3- uptake is associated with changes in histone methylation. Proc Natl Acad Sci U S A. 2011;108 (32):13329-34. doi: 10.1073/pnas.1017863108. PubMed PMID:21788519 PubMed Central PMC3156160.

Krouk, G, Ruffel, S, Gutiérrez, RA, Gojon, A, Crawford, NM, Coruzzi, GM et al.. A framework integrating plant growth with hormones and nutrients. Trends Plant Sci. 2011;16 (4):178-82. doi: 10.1016/j.tplants.2011.02.004. PubMed PMID:21393048 .

Krouk, G, Mirowski, P, LeCun, Y, Shasha, DE, Coruzzi, GM. Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. Genome Biol. 2010;11 (12):R123. doi: 10.1186/gb-2010-11-12-r123. PubMed PMID:21182762 PubMed Central PMC3046483.

Obertello, M, Krouk, G, Katari, MS, Runko, SJ, Coruzzi, GM. Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis. BMC Syst Biol. 2010;4 :111. doi: 10.1186/1752-0509-4-111. PubMed PMID:20704717 PubMed Central PMC2933594.

Cibrián-Jaramillo, A, De la Torre-Bárcena, JE, Lee, EK, Katari, MS, Little, DP, Stevenson, DW et al.. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biol Evol. 2010;2 :225-39. doi: 10.1093/gbe/evq012. PubMed PMID:20624728 PubMed Central PMC2997538.

Vidal, EA, Araus, V, Lu, C, Parry, G, Green, PJ, Coruzzi, GM et al.. Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2010;107 (9):4477-82. doi: 10.1073/pnas.0909571107. PubMed PMID:20142497 PubMed Central PMC2840086.

Krouk, G, Crawford, NM, Coruzzi, GM, Tsay, YF. Nitrate signaling: adaptation to fluctuating environments. Curr Opin Plant Biol. 2010;13 (3):266-73. doi: 10.1016/j.pbi.2009.12.003. PubMed PMID:20093067 .

Nero, D, Katari, MS, Kelfer, J, Tranchina, D, Coruzzi, GM. In silico evaluation of predicted regulatory interactions in Arabidopsis thaliana. BMC Bioinformatics. 2009;10 :435. doi: 10.1186/1471-2105-10-435. PubMed PMID:20025756 PubMed Central PMC2803859.

Katari, MS, Nowicki, SD, Aceituno, FF, Nero, D, Kelfer, J, Thompson, LP et al.. VirtualPlant: a software platform to support systems biology research. Plant Physiol. 2010;152 (2):500-15. doi: 10.1104/pp.109.147025. PubMed PMID:20007449 PubMed Central PMC2815851.

Ruffel, S, Krouk, G, Coruzzi, GM. A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling. Plant Physiol. 2010;152 (2):445-52. doi: 10.1104/pp.109.148502. PubMed PMID:19939945 PubMed Central PMC2815908.

de la Torre-Bárcena, JE, Kolokotronis, SO, Lee, EK, Stevenson, DW, Brenner, ED, Katari, MS et al.. The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS One. 2009;4 (6):e5764. doi: 10.1371/journal.pone.0005764. PubMed PMID:19503618 PubMed Central PMC2685480.

Nero, D, Krouk, G, Tranchina, D, Coruzzi, GM. A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule". BMC Syst Biol. 2009;3 :59. doi: 10.1186/1752-0509-3-59. PubMed PMID:19500399 PubMed Central PMC2702358.

Brenner, ED, Feinberg, P, Runko, S, Coruzzi, GM. A mutation in the Proteosomal Regulatory Particle AAA-ATPase-3 in Arabidopsis impairs the light-specific hypocotyl elongation response elicited by a glutamate receptor agonist, BMAA. Plant Mol Biol. 2009;70 (5):523-33. doi: 10.1007/s11103-009-9489-7. PubMed PMID:19412571 .

Egan, M, Lee, EK, Chiu, JC, Coruzzi, G, Desalle, R. Gene orthology assessment with OrthologID. Methods Mol Biol. 2009;537 :23-38. doi: 10.1007/978-1-59745-251-9_2. PubMed PMID:19378138 .

Krouk, G, Tranchina, D, Lejay, L, Cruikshank, AA, Shasha, D, Coruzzi, GM et al.. A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis. PLoS Comput Biol. 2009;5 (3):e1000326. doi: 10.1371/journal.pcbi.1000326. PubMed PMID:19300494 PubMed Central PMC2652106.

Bender, J, Benfey, P, Bergmann, D, Borevitz, J, Coruzzi, G, Dangl, J et al.. 2020 vision for biology: the role of plants in addressing grand challenges in biology. Mol Plant. 2008;1 (4):561-3. doi: 10.1093/mp/ssn040. PubMed PMID:19825561 .

Thum, KE, Shin, MJ, Gutiérrez, RA, Mukherjee, I, Katari, MS, Nero, D et al.. An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. BMC Syst Biol. 2008;2 :31. doi: 10.1186/1752-0509-2-31. PubMed PMID:18387196 PubMed Central PMC2335094.

Gutiérrez, RA, Stokes, TL, Thum, K, Xu, X, Obertello, M, Katari, MS et al.. Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A. 2008;105 (12):4939-44. doi: 10.1073/pnas.0800211105. PubMed PMID:18344319 PubMed Central PMC2290744.

Sarkar, IN, Egan, MG, Coruzzi, G, Lee, EK, DeSalle, R. Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics. BMC Bioinformatics. 2008;9 :103. doi: 10.1186/1471-2105-9-103. PubMed PMID:18282301 PubMed Central PMC2270260.

Gifford, ML, Dean, A, Gutierrez, RA, Coruzzi, GM, Birnbaum, KD. Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A. 2008;105 (2):803-8. doi: 10.1073/pnas.0709559105. PubMed PMID:18180456 PubMed Central PMC2206617.

Gutiérrez, RA, Gifford, ML, Poultney, C, Wang, R, Shasha, DE, Coruzzi, GM et al.. Insights into the genomic nitrate response using genetics and the Sungear Software System. J Exp Bot. 2007;58 (9):2359-67. doi: 10.1093/jxb/erm079. PubMed PMID:17470441 .

Gutiérrez, RA, Lejay, LV, Dean, A, Chiaromonte, F, Shasha, DE, Coruzzi, GM et al.. Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol. 2007;8 (1):R7. doi: 10.1186/gb-2007-8-1-r7. PubMed PMID:17217541 PubMed Central PMC1839130.

Lejay, LV, Shasha, DE, Palenchar, PM, Kouranov, AY, Cruikshank, AA, Chou, MF et al.. Adaptive combinatorial design to explore large experimental spaces: approach and validation. Syst Biol (Stevenage). 2004;1 (2):206-12. doi: 10.1049/sb:20045020. PubMed PMID:17051692 .

Poultney, CS, Gutiérrez, RA, Katari, MS, Gifford, ML, Paley, WB, Coruzzi, GM et al.. Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics. 2007;23 (2):259-61. doi: 10.1093/bioinformatics/btl496. PubMed PMID:17018536 .

de la Torre, JE, Egan, MG, Katari, MS, Brenner, ED, Stevenson, DW, Coruzzi, GM et al.. ESTimating plant phylogeny: lessons from partitioning. BMC Evol Biol. 2006;6 :48. doi: 10.1186/1471-2148-6-48. PubMed PMID:16776834 PubMed Central PMC1564041.

Chiu, JC, Lee, EK, Egan, MG, Sarkar, IN, Coruzzi, GM, DeSalle, R et al.. OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics. 2006;22 (6):699-707. doi: 10.1093/bioinformatics/btk040. PubMed PMID:16410324 .

Brenner, ED, Katari, MS, Stevenson, DW, Rudd, SA, Douglas, AW, Moss, WN et al.. EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics. 2005;6 :143. doi: 10.1186/1471-2164-6-143. PubMed PMID:16225698 PubMed Central PMC1285361.

Gutiérrez, RA, Shasha, DE, Coruzzi, GM. Systems biology for the virtual plant. Plant Physiol. 2005;138 (2):550-4. doi: 10.1104/pp.104.900150. PubMed PMID:15955912 PubMed Central PMC1150368.

Palenchar, PM, Kouranov, A, Lejay, LV, Coruzzi, GM. Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants. Genome Biol. 2004;5 (11):R91. doi: 10.1186/gb-2004-5-11-r91. PubMed PMID:15535867 PubMed Central PMC545782.

Wang, R, Tischner, R, Gutiérrez, RA, Hoffman, M, Xing, X, Chen, M et al.. Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol. 2004;136 (1):2512-22. doi: 10.1104/pp.104.044610. PubMed PMID:15333754 PubMed Central PMC523318.

Thum, KE, Shin, MJ, Palenchar, PM, Kouranov, A, Coruzzi, GM. Genome-wide investigation of light and carbon signaling interactions in Arabidopsis. Genome Biol. 2004;5 (2):R10. doi: 10.1186/gb-2004-5-2-r10. PubMed PMID:14759260 PubMed Central PMC395748.

Wong, HK, Chan, HK, Coruzzi, GM, Lam, HM. Correlation of ASN2 gene expression with ammonium metabolism in Arabidopsis. Plant Physiol. 2004;134 (1):332-8. doi: 10.1104/pp.103.033126. PubMed PMID:14671018 PubMed Central PMC316312.

Brenner, ED, Stevenson, DW, McCombie, RW, Katari, MS, Rudd, SA, Mayer, KF et al.. Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biol. 2003;4 (12):R78. doi: 10.1186/gb-2003-4-12-r78. PubMed PMID:14659015 PubMed Central PMC329417.

Raikhel, NV, Coruzzi, GM. Achieving the in silico plant. Systems biology and the future of plant biological research. Plant Physiol. 2003;132 (2):404-9. . PubMed PMID:12822566 PubMed Central PMC1540317.

Lam, HM, Wong, P, Chan, HK, Yam, KM, Chen, L, Chow, CM et al.. Overexpression of the ASN1 gene enhances nitrogen status in seeds of Arabidopsis. Plant Physiol. 2003;132 (2):926-35. doi: 10.1104/pp.103.020123. PubMed PMID:12805621 PubMed Central PMC167031.

Thum, KE, Shasha, DE, Lejay, LV, Coruzzi, GM. Light- and carbon-signaling pathways. Modeling circuits of interactions. Plant Physiol. 2003;132 (2):440-52. doi: 10.1104/pp.103.022780. PubMed PMID:12805577 PubMed Central PMC166987.

Oliveira, IC, Brears, T, Knight, TJ, Clark, A, Coruzzi, GM. Overexpression of cytosolic glutamine synthetase. Relation to nitrogen, light, and photorespiration. Plant Physiol. 2002;129 (3):1170-80. doi: 10.1104/pp.020013. PubMed PMID:12114571 PubMed Central PMC166511.

Chiu, JC, Brenner, ED, DeSalle, R, Nitabach, MN, Holmes, TC, Coruzzi, GM et al.. Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana. Mol Biol Evol. 2002;19 (7):1066-82. doi: 10.1093/oxfordjournals.molbev.a004165. PubMed PMID:12082126 .

Miesak, BH, Coruzzi, GM. Molecular and physiological analysis of Arabidopsis mutants defective in cytosolic or chloroplastic aspartate aminotransferase. Plant Physiol. 2002;129 (2):650-60. doi: 10.1104/pp.005090. PubMed PMID:12068109 PubMed Central PMC161691.

Lancien, M, Martin, M, Hsieh, MH, Leustek, T, Goodman, H, Coruzzi, GM et al.. Arabidopsis glt1-T mutant defines a role for NADH-GOGAT in the non-photorespiratory ammonium assimilatory pathway. Plant J. 2002;29 (3):347-58. doi: 10.1046/j.1365-313x.2002.01218.x. PubMed PMID:11844111 .

Shasha, DE, Kouranov, AY, Lejay, LV, Chou, MF, Coruzzi, GM. Using combinatorial design to study regulation by multiple input signals. A tool for parsimony in the post-genomics era. Plant Physiol. 2001;127 (4):1590-4. . PubMed PMID:11743103 PubMed Central PMC1540192.

Lacombe, B, Becker, D, Hedrich, R, DeSalle, R, Hollmann, M, Kwak, JM et al.. The identity of plant glutamate receptors. Science. 2001;292 (5521):1486-7. doi: 10.1126/science.292.5521.1486b. PubMed PMID:11379626 .

Oliveira, IC, Brenner, E, Chiu, J, Hsieh, MH, Kouranov, A, Lam, HM et al.. Metabolite and light regulation of metabolism in plants: lessons from the study of a single biochemical pathway. Braz J Med Biol Res. 2001;34 (5):567-75. doi: 10.1590/s0100-879x2001000500003. PubMed PMID:11323742 .

Coruzzi, GM, Zhou, L. Carbon and nitrogen sensing and signaling in plants: emerging 'matrix effects'. Curr Opin Plant Biol. 2001;4 (3):247-53. doi: 10.1016/s1369-5266(00)00168-0. PubMed PMID:11312136 .

Coruzzi, G, Bush, DR. Nitrogen and carbon nutrient and metabolite signaling in plants. Plant Physiol. 2001;125 (1):61-4. doi: 10.1104/pp.125.1.61. PubMed PMID:11154297 PubMed Central PMC1539326.

Brenner, ED, Martinez-Barboza, N, Clark, AP, Liang, QS, Stevenson, DW, Coruzzi, GM et al.. Arabidopsis mutants resistant to S(+)-beta-methyl-alpha, beta-diaminopropionic acid, a cycad-derived glutamate receptor agonist. Plant Physiol. 2000;124 (4):1615-24. doi: 10.1104/pp.124.4.1615. PubMed PMID:11115879 PubMed Central PMC59860.

Chory, J, Ecker, JR, Briggs, S, Caboche, M, Coruzzi, GM, Cook, D et al.. National Science Foundation-Sponsored Workshop Report: "The 2010 Project" functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them. Plant Physiol. 2000;123 (2):423-6. doi: 10.1104/pp.123.2.423. PubMed PMID:10859172 PubMed Central PMC1539254.

Oliveira, IC, Coruzzi, GM. Carbon and amino acids reciprocally modulate the expression of glutamine synthetase in Arabidopsis. Plant Physiol. 1999;121 (1):301-10. doi: 10.1104/pp.121.1.301. PubMed PMID:10482686 PubMed Central PMC59385.

Chiu, J, DeSalle, R, Lam, HM, Meisel, L, Coruzzi, G. Molecular evolution of glutamate receptors: a primitive signaling mechanism that existed before plants and animals diverged. Mol Biol Evol. 1999;16 (6):826-38. doi: 10.1093/oxfordjournals.molbev.a026167. PubMed PMID:10368960 .

Lam, HM, Hsieh, MH, Coruzzi, G. Reciprocal regulation of distinct asparagine synthetase genes by light and metabolites in Arabidopsis thaliana. Plant J. 1998;16 (3):345-53. doi: 10.1046/j.1365-313x.1998.00302.x. PubMed PMID:9881155 .

Lam, HM, Chiu, J, Hsieh, MH, Meisel, L, Oliveira, IC, Shin, M et al.. Glutamate-receptor genes in plants. Nature. 1998;396 (6707):125-6. doi: 10.1038/24066. PubMed PMID:9823891 .

Hsieh, MH, Lam, HM, van de Loo, FJ, Coruzzi, G. A PII-like protein in Arabidopsis: putative role in nitrogen sensing. Proc Natl Acad Sci U S A. 1998;95 (23):13965-70. doi: 10.1073/pnas.95.23.13965. PubMed PMID:9811909 PubMed Central PMC24990.

Schultz, CJ, Hsu, M, Miesak, B, Coruzzi, GM. Arabidopsis mutants define an in vivo role for isoenzymes of aspartate aminotransferase in plant nitrogen assimilation. Genetics. 1998;149 (2):491-9. doi: 10.1093/genetics/149.2.491. PubMed PMID:9611168 PubMed Central PMC1460188.

Coschigano, KT, Melo-Oliveira, R, Lim, J, Coruzzi, GM. Arabidopsis gls mutants and distinct Fd-GOGAT genes. Implications for photorespiration and primary nitrogen assimilation. Plant Cell. 1998;10 (5):741-52. doi: 10.1105/tpc.10.5.741. PubMed PMID:9596633 PubMed Central PMC144371.

Ngai, N, Tsai, FY, Coruzzi, G. Light-induced transcriptional repression of the pea AS1 gene: identification of cis-elements and transfactors. Plant J. 1997;12 (5):1021-34. doi: 10.1046/j.1365-313x.1997.12051021.x. PubMed PMID:9418044 .

Lam, HM, Coschigano, KT, Oliveira, IC, Melo-Oliveira, R, Coruzzi, GM. THE MOLECULAR-GENETICS OF NITROGEN ASSIMILATION INTO AMINO ACIDS IN HIGHER PLANTS. Annu Rev Plant Physiol Plant Mol Biol. 1996;47 :569-593. doi: 10.1146/annurev.arplant.47.1.569. PubMed PMID:15012301 .

Melo-Oliveira, R, Oliveira, IC, Coruzzi, GM. Arabidopsis mutant analysis and gene regulation define a nonredundant role for glutamate dehydrogenase in nitrogen assimilation. Proc Natl Acad Sci U S A. 1996;93 (10):4718-23. doi: 10.1073/pnas.93.10.4718. PubMed PMID:8643469 PubMed Central PMC39345.

Walker, EL, Weeden, NF, Taylor, CB, Green, P, Coruzzi, GM. Molecular evolution of duplicate copies of genes encoding cytosolic glutamine synthetase in Pisum sativum. Plant Mol Biol. 1995;29 (6):1111-25. doi: 10.1007/BF00020456. PubMed PMID:8616212 .

Lam, HM, Coschigano, K, Schultz, C, Melo-Oliveira, R, Tjaden, G, Oliveira, I et al.. Use of Arabidopsis mutants and genes to study amide amino acid biosynthesis. Plant Cell. 1995;7 (7):887-98. doi: 10.1105/tpc.7.7.887. PubMed PMID:7640525 PubMed Central PMC160882.

Tjaden, G, Edwards, JW, Coruzzi, GM. Cis elements and trans-acting factors affecting regulation of a nonphotosynthetic light-regulated gene for chloroplast glutamine synthetase. Plant Physiol. 1995;108 (3):1109-17. doi: 10.1104/pp.108.3.1109. PubMed PMID:7630938 PubMed Central PMC157463.

Schultz, CJ, Coruzzi, GM. The aspartate aminotransferase gene family of Arabidopsis encodes isoenzymes localized to three distinct subcellular compartments. Plant J. 1995;7 (1):61-75. doi: 10.1046/j.1365-313x.1995.07010061.x. PubMed PMID:7894512 .

Lam, HM, Peng, SS, Coruzzi, GM. Metabolic regulation of the gene encoding glutamine-dependent asparagine synthetase in Arabidopsis thaliana. Plant Physiol. 1994;106 (4):1347-57. doi: 10.1104/pp.106.4.1347. PubMed PMID:7846154 PubMed Central PMC159672.

Tjaden, G, Coruzzi, GM. A novel AT-rich DNA binding protein that combines an HMG I-like DNA binding domain with a putative transcription domain. Plant Cell. 1994;6 (1):107-18. doi: 10.1105/tpc.6.1.107. PubMed PMID:7907505 PubMed Central PMC160420.

Brears, T, Liu, C, Knight, TJ, Coruzzi, GM. Ectopic Overexpression of Asparagine Synthetase in Transgenic Tobacco. Plant Physiol. 1993;103 (4):1285-1290. doi: 10.1104/pp.103.4.1285. PubMed PMID:12232020 PubMed Central PMC159117.

Coruzzi, GM, Last, RL. A Crucial Role for the NSF Postdoctoral Fellowship Program in Plant Biology. Plant Cell. 1993;5 (7):722. doi: 10.1105/tpc.5.7.722. PubMed PMID:12271083 PubMed Central PMC160310.

McGrath, RB, Coruzzi, GM. A gene network controlling glutamine and asparagine biosynthesis in plants. Plant J. 1991;1 (3):275-80. doi: 10.1046/j.1365-313x.1991.00999.x. PubMed PMID:1688250 .

Tsai, FY, Coruzzi, G. Light represses transcription of asparagine synthetase genes in photosynthetic and nonphotosynthetic organs of plants. Mol Cell Biol. 1991;11 (10):4966-72. doi: 10.1128/mcb.11.10.4966-4972.1991. PubMed PMID:1681424 PubMed Central PMC361478.

Brears, T, Walker, EL, Coruzzi, GM. A promoter sequence involved in cell-specific expression of the pea glutamine synthetase GS3A gene in organs of transgenic tobacco and alfalfa. Plant J. 1991;1 (2):235-44. doi: 10.1111/j.1365-313x.1991.00235.x. PubMed PMID:1688248 .

Edwards, JW, Walker, EL, Coruzzi, GM. Cell-specific expression in transgenic plants reveals nonoverlapping roles for chloroplast and cytosolic glutamine synthetase. Proc Natl Acad Sci U S A. 1990;87 (9):3459-63. doi: 10.1073/pnas.87.9.3459. PubMed PMID:1970638 PubMed Central PMC53920.

Tsai, FY, Coruzzi, GM. Dark-induced and organ-specific expression of two asparagine synthetase genes in Pisum sativum. EMBO J. 1990;9 (2):323-32. doi: 10.1002/j.1460-2075.1990.tb08114.x. PubMed PMID:1968003 PubMed Central PMC551669.

Edwards, JW, Coruzzi, GM. Cell-specific gene expression in plants. Annu Rev Genet. 1990;24 :275-303. doi: 10.1146/ PubMed PMID:2088170 .

Walker, EL, Coruzzi, GM. Developmentally Regulated Expression of the Gene Family for Cytosolic Glutamine Synthetase in Pisum sativum. Plant Physiol. 1989;91 (2):702-8. doi: 10.1104/pp.91.2.702. PubMed PMID:16667090 PubMed Central PMC1062059.

Edwards, JW, Coruzzi, GM. Photorespiration and light act in concert to regulate the expression of the nuclear gene for chloroplast glutamine synthetase. Plant Cell. 1989;1 (2):241-8. doi: 10.1105/tpc.1.2.241. PubMed PMID:2577725 PubMed Central PMC159756.

Tingey, SV, Tsai, FY, Edwards, JW, Walker, EL, Coruzzi, GM. Chloroplast and cytosolic glutamine synthetase are encoded by homologous nuclear genes which are differentially expressed in vivo. J Biol Chem. 1988;263 (20):9651-7. . PubMed PMID:2898472 .

Tingey, SV, Coruzzi, GM. Glutamine Synthetase of Nicotiana plumbaginifolia: Cloning and in Vivo Expression. Plant Physiol. 1987;84 (2):366-73. doi: 10.1104/pp.84.2.366. PubMed PMID:16665445 PubMed Central PMC1056585.

Tingey, SV, Walker, EL, Coruzzi, GM. Glutamine synthetase genes of pea encode distinct polypeptides which are differentially expressed in leaves, roots and nodules. EMBO J. 1987;6 (1):1-9. doi: 10.1002/j.1460-2075.1987.tb04710.x. PubMed PMID:2884100 PubMed Central PMC553348.

Fluhr, R, Moses, P, Morelli, G, Coruzzi, G, Chua, NH. Expression dynamics of the pea rbcS multigene family and organ distribution of the transcripts. EMBO J. 1986;5 (9):2063-2071. doi: 10.1002/j.1460-2075.1986.tb04467.x. PubMed PMID:16453702 PubMed Central PMC1167083.

Broglie, R, Coruzzi, G, Keith, B, Chua, NH. Molecular biology of C4 photosynthesis in Zea mays: differential localization of proteins and mRNAs in the two leaf cell types. Plant Mol Biol. 1984;3 (6):431-44. doi: 10.1007/BF00033391. PubMed PMID:24310577 .

Coruzzi, G, Broglie, R, Edwards, C, Chua, NH. Tissue-specific and light-regulated expression of a pea nuclear gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase. EMBO J. 1984;3 (8):1671-9. doi: 10.1002/j.1460-2075.1984.tb02031.x. PubMed PMID:6479146 PubMed Central PMC557581.

Broglie, R, Coruzzi, G, Fraley, RT, Rogers, SG, Horsch, RB, Niedermeyer, JG et al.. Light-regulated expression of a pea ribulose-1,5-bisphosphate carboxylase small subunit gene in transformed plant cells. Science. 1984;224 (4651):838-43. doi: 10.1126/science.6719112. PubMed PMID:6719112 .

Coruzzi, G, Broglie, R, Cashmore, A, Chua, NH. Nucleotide sequences of two pea cDNA clones encoding the small subunit of ribulose 1,5-bisphosphate carboxylase and the major chlorophyll a/b-binding thylakoid polypeptide. J Biol Chem. 1983;258 (3):1399-402. . PubMed PMID:6296093 .

Coruzzi, G, Bonitz, SG, Thalenfeld, BE, Tzagoloff, A. Assembly of the mitochondrial membrane system. Analysis of the nucleotide sequence and transcripts in the oxi1 region of yeast mitochondrial DNA. J Biol Chem. 1981;256 (24):12780-7. . PubMed PMID:7031051 .

Bonitz, SG, Coruzzi, G, Thalenfeld, BE, Tzagoloff, A, Macino, G. Assembly of the mitochondrial membrane system. Structure and nucleotide sequence of the gene coding for subunit 1 of yeast cytochrme oxidase. J Biol Chem. 1980;255 (24):11927-41. . PubMed PMID:6254986 .

Bonitz, SG, Coruzzi, G, Thalenfeld, BE, Tzagoloff, A, Macino, G. Assembly of the mitochondrial membrane system. Physical map of the Oxi3 locus of yeast mitochondrial DNA. J Biol Chem. 1980;255 (24):11922-6. . PubMed PMID:6254985 .

Berlani, RE, Bonitz, SG, Coruzzi, G, Nobrega, M, Tzagoloff, A. Transfer RNA genes in the cap-oxil region of yeast mitochondrial DNA. Nucleic Acids Res. 1980;8 (21):5017-30. doi: 10.1093/nar/8.21.5017. PubMed PMID:7003547 PubMed Central PMC324276.

Bonitz, SG, Berlani, R, Coruzzi, G, Li, M, Macino, G, Nobrega, FG et al.. Codon recognition rules in yeast mitochondria. Proc Natl Acad Sci U S A. 1980;77 (6):3167-70. doi: 10.1073/pnas.77.6.3167. PubMed PMID:6997870 PubMed Central PMC349575.

Coruzzi, G, Tzagoloff, A. Assembly of the mitochondrial membrane system. DNA sequence of subunit 2 of yeast cytochrome oxidase. J Biol Chem. 1979;254 (18):9324-30. . PubMed PMID:225327 .

Macino, G, Coruzzi, G, Nobrega, FG, Li, M, Tzagoloff, A. Use of the UGA terminator as a tryptophan codon in yeast mitochondria. Proc Natl Acad Sci U S A. 1979;76 (8):3784-5. doi: 10.1073/pnas.76.8.3784. PubMed PMID:226981 PubMed Central PMC383918.

Coruzzi, G, Trembath, MK, Tzagoloff, A. Assembly of the mitochondrial membrane system: mutations in the pho2 locus of the mitochondrial genome of Saccharomyces cerevisiae. Eur J Biochem. 1978;92 (1):279-87. doi: 10.1111/j.1432-1033.1978.tb12746.x. PubMed PMID:153229 .

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