Gloria Coruzzi

Plant systems biology and evolutionary genomics

Plant Systems Biology. Our goal is to identify gene regulatory networks in plants using a combination of genetic, genomic, bioinformatic, and systems biological approaches. Our lab has two main areas of inquiry: 1. A systems approach to nitrogen networks & the Virtual Plant; 2. Comparative Genomics of Seed Evolution.

A Systems Approach to Nitrogen Networks & the VirtualPlant.
The long term goal of this project is to understand how internal and external perturbations affect gene regulatory networks that link plant metabolism and development. Succeeding in this endeavor will allow us to (1) explain mechanistically how changes in gene networks evoke systems-wide responses to external treatments such as nitrogen, and (2) to predict network states under untested conditions or in response to modifications. In the long term, this systems biology approach to gene networks should enable researchers to test the effects of biotechnological strategies for gene modifications in silico, prior to implementation in transgenic plants.  Our approach starts with the integration of all available information on Arabidopsis genomic data into a "multinetwork" where the "edges" connecting gene "nodes" are supported by multiple evidence including: metabolic pathway connections, protein:protein and protein:DNA interactions, microarray data, microRNA:target datasets, and literature-based interactions.  At present, the Arabidopsis multinetwork we have created  contains approximately 7,000 gene nodes and 230,000 interactions between them.  As proof-of-principle, we have used this Arabidopsis multinetwork to identify the gene networks controlled by light, carbon and nitrogen signals.   In selected cases, the networks identified in wild-type plants have been validated using microarray data from Arabidopsis signaling mutants.  Our studies include analysis of gene networks in specific organs (leaves, roots or seeds) or in specific cell-types based on analysis of microarray data obtained from cell-sorted samples of roots.  The network analysis of gene lists generated from the microarray data in a network view is shown in Figure 1.

FIGURE 1. Nitrogen Networks and the VirtualPlant

The VirtualPlant Project.  In order to go beyond data integration to conceptual integration of genomic data, we recognize that scientists pattern recognition skills often lead to the most enduring qualitative biological insights. To support those skills in a data-rich environment, have implemented a set of data integration, analysis and visualization tools into a system called the "VirtualPlant" (www.virtualplant.org).   This system encompasses visualization techniques that render the multivariate genomic information in visual formats that facilitate the extraction of biological concepts and enable a "Systems Biology" view of the genomic data.  While our project relates specifically to Arabidopsis, the data structures, algorithms, and visualization tools we have developed have been designed in a species-independent fashion.  Thus, with the proper data uploads, the system can be used to visualize and model the molecular basis and underlying genomic responses in any organism for which genomic data is available.

Comparative Genomics of Seed Evolution
This NSF Plant Genome project (NSF DBI-0421604) involves the comparative genomic analysis of non-model, non-crop species, to uncover genes important to the evolution of seeds, an important agronomic trait. This project is being conducted with our partners in the NY Plant Genomic Consortium that include coPIs from NYU Biology (Coruzzi), NYU Courant (Shasha), NYBG (Stevenson), AMNH (DeSalle) and CSHL (McCombie & Martienssen).   Our approach is to generate and mine EST data from the the most primitive living-seed plants, the nodal Gymnosperms and the heterosporous lycophyte, Selaginella (as an outgroup), to resolve their phylogenetic relationship and to uncover novel genes and characters associated with the evolution and development of seeds. This project is being conducted collaboratively by scientists at three NY area institutions specializing in evolution, genomics and bioinformatics, who comprise The New York Plant Genomics Consortium (www.nypgenomics.org).  Participants in this project include PIs who collaborate in the training of post docs and graduate students from New York University, The New York Botanical Garden, Cold Spring Harbor, and The American Museum of Natural History.  We aim to achieve three goals: 

1. Evolutionary Genomics: We have generated 18,437 ESTs from three "nodal" Gymnosperm species which have enabled us to create genome-scale phylogenies to resolve evolutionary relationships in the Gymnosperms and identify putative genes involved in the evolution of seeds.
2. Phylogenomics/Informatics: We developed new informatic tools to automate orthology determination in a parsimony framework and the construction of phylogenomic scale trees.  These tools include: and Ortholog ID, ViCoGenta (Viewer for Comparing Genomes to Arabidopsis), and a newer tool under development ASAP (Automatic Systematic Analysis Program).
3. Functional Genomics: To test the function of genes supporting the node for seed plant evolution we have begun to test the expression in Gymnosperm tissues (RNA and in situs) and perform analysis of Arabidopsis mutants in orthologous genes. 

FIGURE 2. Comparative Genomics of Seed Evolution: Use of ESTs in functional phylogenomic studies to identify genes associated with the evolution of seeds

DOE-BER: DE-SC0014377 (08/15/2015 – 08/14/2020)
Department of Energy, Biological and Environmental Research
Title: EvoNet: A Phylogenomic and Systems Biology Approach to Identify Genes Underlying Plant Survival in Marginal, Low-N Soils.
PI: Coruzzi
Co-PIs: R. Gutiérrez (Pontificia Universidad Católica de Chile), D. Stevenson (New York Botanical Garden), R. DeSalle (American Museum of Natural History), W.R. McCombie (Cold Spring Harbor Laboratory), JM Ané & Heidi Kaeppler (University of Wisconsin–Madison)
http://genomicscience.energy.gov/sustainability/SustainabilityAwards_15flyer.pdf

NSF-PGRP: IOS-1339362 (09/01/2014 – 08/31/2018)
National Science Foundation, Integrative Organismal Systems
Title: NSF Plant Genome: NutriNet: A Network Inspired Approach to Improving Nutrient Use Efficiency (NUE) in Crop
PI: Coruzzi
Co-PIs: Dennis Shasha (NYU Courant), Stephen Moose (Univ. Illinois)

NSF - MCB-1412232 (07/01/2014 – 06/30/2017)
National Science Foundation, Molecular and Cellular Biosciences
Title: Prospecting for Resources: A Systems Integration of Local and Systemic Nutrient Signaling
PI: Coruzzi
Co-PI: Dennis Shasha (NYU Courant)

DOE-BES: DE-FG02-92ER20071 (12/1/2014 – 5/31/2017)
Department of Energy, Energy Biosciences
Title: Asparagine Synthetase Gene Regulatory Network and Plant Nitrogen Metabolism
PI: Coruzzi

Gloria Coruzzi is currently the Carroll & Milton Petrie Professor of Biology at New York University. Her research in Plant Systems Biology combines genomic, bioinformatic and system biology approaches to identify gene networks involved in biological regulatory mechanisms controlling nitrogen use and the evolution of seeds. A native New Yorker, Dr. Coruzzi received her Ph.D. in Molecular & Cell Biology at New York University School of Medicine in yeast genetics where she decoded the yeast mitochondrial genome. Her studies on plant genes began during her studies as an Assistant and Associate Professor at Rockefeller University. Since joining NYU a Professor, Dr. Coruzzi's lab initiated Plant Systems Biology approaches to perform functional genomic studies in Arabidopsis and other species. This work including the development of new informatic tools encompassed in a software platform called VirtualPlant (www.virtualplant.org) which is being performed in collaboration with colleagues at NYU Courant Institute for Math & Computer Science. Dr. Coruzzi is also engaged in a collaborative genomic project on the Comparative Genomics of Seed Evolution with co-PIs at the New York Botanical Garden, the American Museum of Natural History and Cold Spring Harbor labs. Dr. Coruzzi's research is funded by The National Institutes of Health, The NSF 2010 Project, The NSF Plant Genome Project, the NSF Database and Information Project, and The Department of Energy. Dr. Coruzzi was named an American Association for the Advancement of Science Fellow in 2005, a Fellow of the American Society of Plant Biology in 2010, was awarded the ASPB Stephen Hales Prize in 2016, and currently serves on several science editorial and advisory boards including the Arabidopsis information Portal, and JGI Plant Program Advisory Board.

Becoming A Scientist
BIOL-UA 995 Offered each Fall
Course Overview: Pursuing a scientific career is intellectually exciting and practically important to society.  Succeeding in a scientific career is both an art and a science.  Being successful requires intelligence and expertise in the laboratory, but equally important, it requires skills in scientific writing, oral communication, and ethics.  In this course, “Becoming a Scientist”, undergraduate Biology majors who are conducting independent laboratory-based research projects will perform project-based learning through reading scientific papers, and through writing and oral communication of scientific results, while also gaining exposure to issues in scientific ethics and career paths.  Each student will develop these skills using their honors thesis research project as a springboard.

Senior Honor’s Thesis Course
BIOL-UA 999 Offered each Spring
Course Objectives: Each student will write and defend an honor’s thesis based on independent research and the skills developed in BIOL-UA995 “Becoming a Scientist.”

Date of these PubMed search results: March 24 2020
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1. Nitrate 2020: Thirty years from transport to signaling networks.
   Plant Cell (2020 Mar 13) PMID: 32169959
   Vidal EA, Alvarez JM, Araus V, Riveras E, Brooks M, Krouk G, Ruffel S, Lejay L, Crawford N, Coruzzi GM, Gutierrez RA
2. Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade.
   Nat Commun (2020 Mar 2) PMC7052136 free full-text archive
   Alvarez JM, Schinke AL, Brooks MD, Pasquino A, Leonelli L, Varala K, Safi A, Krouk G, Krapp A, Coruzzi GM
3. A balancing act: how plants integrate nitrogen and water signals.
   J Exp Bot (2020 Jan 28) PMID: 31990028
   Araus V, Swift J, Alvarez JM, Henry A, Coruzzi GM
4. SDG8-Mediated Histone Methylation and RNA Processing Function in the Response to Nitrate Signaling.
   Plant Physiol (2020 Jan) PMC6945839 free full-text archive
   Li Y, Brooks M, Yeoh‑Wang J, McCoy RM, Rock TM, Pasquino A, Moon CI, Patrick RM, Tanurdzic M, Ruffel S, Widhalm JR, McCombie WR, Coruzzi GM
5. WRKY1 Mediates Transcriptional Regulation of Light and Nitrogen Signaling Pathways.
   Plant Physiol (2019 Nov) PMC6836853 free full-text archive
   Heerah S, Katari M, Penjor R, Coruzzi G, Marshall‑Colon A
6. iPlant Systems Biology (iPSB): An International Network Hub in the Plant Community.
   Mol Plant (2019 Jun 3) PMID: 31125688
   Falter‑Braun P, Brady S, Gutierrez RA, Coruzzi GM, Krouk G
7. Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions.
   Nat Commun (2019 Apr 5) PMC6451032 free full-text archive
   Brooks MD, Cirrone J, Pasquino AV, Alvarez JM, Swift J, Mittal S, Juang CL, Varala K, Gutierrez RA, Krouk G, Shasha D, Coruzzi GM
8. Water impacts nutrient dose responses genome-wide to affect crop production.
   Nat Commun (2019 Mar 26) PMC6435674 free full-text archive
   Swift J, Adame M, Tranchina D, Henry A, Coruzzi GM
9. Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants.
   Proc Natl Acad Sci U S A (2018 Jun 19) PMC6016767 free full-text archive
   Varala K, Marshall‑Colon A, Cirrone J, Brooks MD, Pasquino AV, Leran S, Mittal S, Rock TM, Edwards MB, Kim GJ, Ruffel S, McCombie WR, Shasha D, Coruzzi GM
10. muChIP-Seq for Genome-Wide Mapping of In Vivo TF-DNA Interactions in Arabidopsis Root Protoplasts.
    Methods Mol Biol (2018) PMID: 29525963
    Para A, Li Y, Coruzzi GM
11. Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture.
    Plant Cell (2017 Oct) PMC5774560 free full-text archive
    Walker L, Boddington C, Jenkins D, Wang Y, Gronlund JT, Hulsmans J, Kumar S, Patel D, Moore JD, Carter A, Samavedam S, Bonomo G, Hersh DS, Coruzzi GM, Burroughs NJ, Gifford ML
12. Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root.
    Sci Signal (2016 Oct 25) PMID: 27811143
    Ristova D, Carre C, Pervent M, Medici A, Kim GJ, Scalia D, Ruffel S, Birnbaum KD, Lacombe B, Busch W, Coruzzi GM, Krouk G
13. A matter of time - How transient transcription factor interactions create dynamic gene regulatory networks.
    Biochim Biophys Acta Gene Regul Mech (2017 Jan) PMC5203810 free full-text archive
    Swift J, Coruzzi GM
14. Nitrate Transport, Sensing, and Responses in Plants.
    Mol Plant (2016 Jun 6) PMID: 27212387
    O'Brien JA, Vega A, Bouguyon E, Krouk G, Gojon A, Coruzzi G, Gutierrez RA
15. "Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run".
    BMC Genomics (2016 Feb 3) PMC4738784 free full-text archive
    Doidy J, Li Y, Neymotin B, Edwards MB, Varala K, Gresham D, Coruzzi GM
16. Long-distance nitrate signaling displays cytokinin dependent and independent branches.
    J Integr Plant Biol (2016 Mar) PMID: 26619818
    Ruffel S, Poitout A, Krouk G, Coruzzi GM, Lacombe B
17. "Hit-and-Run" leaves its mark: catalyst transcription factors and chromatin modification.
    Bioessays (2015 Aug) PMC4548861 free full-text archive
    Varala K, Li Y, Marshall‑Colon A, Para A, Coruzzi GM
18. From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks.
    Trends Genet (2015 Sep) PMC4558309 free full-text archive
    Li Y, Varala K, Coruzzi GM
19. Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice.
    Plant Physiol (2015 Aug) PMC4528727 free full-text archive
    Obertello M, Shrivastava S, Katari MS, Coruzzi GM
20. The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants.
    Genome Biol (2015 Apr 19) PMC4464704 free full-text archive
    Li Y, Mukherjee I, Thum KE, Tanurdzic M, Katari MS, Obertello M, Edwards MB, McCombie WR, Martienssen RA, Coruzzi GM
21. AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip.
    Nat Commun (2015 Feb 27) PMC4373655 free full-text archive
    Medici A, Marshall‑Colon A, Ronzier E, Szponarski W, Wang R, Gojon A, Crawford NM, Ruffel S, Coruzzi GM, Krouk G
22. Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution.
    PLoS Genet (2014 Jul) PMC4102449 free full-text archive
    Delaux PM, Varala K, Edger PP, Coruzzi GM, Pires JC, Ane JM
23. Finding a nitrogen niche: a systems integration of local and systemic nitrogen signalling in plants.
    J Exp Bot (2014 Oct) PMID: 24963003
    Li Y, Krouk G, Coruzzi GM, Ruffel S
24. Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis.
    Proc Natl Acad Sci U S A (2014 Jul 15) PMC4104873 free full-text archive
    Para A, Li Y, Marshall‑Colon A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM
25. Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots.
    BMC Genomics (2013 Oct 11) PMC3906980 free full-text archive
    Vidal EA, Moyano TC, Krouk G, Katari MS, Tanurdzic M, McCombie WR, Coruzzi GM, Gutierrez RA
26. A unified nomenclature of NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family members in plants.
    Trends Plant Sci (2014 Jan) PMID: 24055139
    Leran S, Varala K, Boyer JC, Chiurazzi M, Crawford N, Daniel‑Vedele F, David L, Dickstein R, Fernandez E, Forde B, Gassmann W, Geiger D, Gojon A, Gong JM, Halkier BA, Harris JM, Hedrich R, Limami AM, Rentsch D, Seo M, Tsay YF, Zhang M, Coruzzi G, Lacombe B
27. Plasticity regulators modulate specific root traits in discrete nitrogen environments.
    PLoS Genet (2013) PMC3764102 free full-text archive
    Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD
28. Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture.
    Proc Natl Acad Sci U S A (2013 Sep 10) PMC3773737 free full-text archive
    Rosas U, Cibrian‑Jaramillo A, Ristova D, Banta JA, Gifford ML, Fan AH, Zhou RW, Kim GJ, Krouk G, Birnbaum KD, Purugganan MD, Coruzzi GM
29. Gene regulatory networks in plants: learning causality from time and perturbation.
    Genome Biol (2013 Jun 27) PMC3707030 free full-text archive
    Krouk G, Lingeman J, Colon AM, Coruzzi G, Shasha D
30. TARGET: a transient transformation system for genome-wide transcription factor target discovery.
    Mol Plant (2013 May) PMC3660954 free full-text archive
    Bargmann BO, Marshall‑Colon A, Efroni I, Ruffel S, Birnbaum KD, Coruzzi GM, Krouk G
31. RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis.
    Plant Physiol (2013 Mar) PMC3585581 free full-text archive
    Ristova D, Rosas U, Krouk G, Ruffel S, Birnbaum KD, Coruzzi GM
32. A functional phylogenomic view of the seed plants.
    PLoS Genet (2011 Dec) PMC3240601 free full-text archive
    Lee EK, Cibrian‑Jaramillo A, Kolokotronis SO, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, Desalle R
33. 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 Nov 8) PMC3215050 free full-text archive
    Ruffel S, Krouk G, Ristova D, Shasha D, Birnbaum KD, Coruzzi GM
34. 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 Aug 9) PMC3156160 free full-text archive
    Widiez T, El Kafafi el S, Girin T, Berr A, Ruffel S, Krouk G, Vayssieres A, Shen WH, Coruzzi GM, Gojon A, Lepetit M
35. A framework integrating plant growth with hormones and nutrients.
    Trends Plant Sci (2011 Apr) PMID: 21393048
    Krouk G, Ruffel S, Gutierrez RA, Gojon A, Crawford NM, Coruzzi GM, Lacombe B
36. Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate.
    Genome Biol (2010) PMC3046483 free full-text archive
    Krouk G, Mirowski P, LeCun Y, Shasha DE, Coruzzi GM
37. Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis.
    BMC Syst Biol (2010 Aug 12) PMC2933594 free full-text archive
    Obertello M, Krouk G, Katari MS, Runko SJ, Coruzzi GM
38. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution.
    Genome Biol Evol (2010 Jul 12) PMC2997538 free full-text archive
    Cibrian‑Jaramillo A, De la Torre‑Barcena JE, Lee EK, Katari MS, Little DP, Stevenson DW, Martienssen R, Coruzzi GM, DeSalle R
39. Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana.
    Proc Natl Acad Sci U S A (2010 Mar 2) PMC2840086 free full-text archive
    Vidal EA, Araus V, Lu C, Parry G, Green PJ, Coruzzi GM, Gutierrez RA
40. Nitrate signaling: adaptation to fluctuating environments.
    Curr Opin Plant Biol (2010 Jun) PMID: 20093067
    Krouk G, Crawford NM, Coruzzi GM, Tsay YF
41. In silico evaluation of predicted regulatory interactions in Arabidopsis thaliana.
    BMC Bioinformatics (2009 Dec 21) PMC2803859 free full-text archive
    Nero D, Katari MS, Kelfer J, Tranchina D, Coruzzi GM
42. VirtualPlant: a software platform to support systems biology research.
    Plant Physiol (2010 Feb) PMC2815851 free full-text archive
    Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutierrez RA
43. A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling.
    Plant Physiol (2010 Feb) PMC2815908 free full-text archive
    Ruffel S, Krouk G, Coruzzi GM
44. The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.
    PLoS One (2009 Jun 2) PMC2685480 free full-text archive
    de la Torre‑Barcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R
45. A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule".
    BMC Syst Biol (2009 Jun 6) PMC2702358 free full-text archive
    Nero D, Krouk G, Tranchina D, Coruzzi GM
46. 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 Jul) PMID: 19412571
    Brenner ED, Feinberg P, Runko S, Coruzzi GM
47. Gene orthology assessment with OrthologID.
    Methods Mol Biol (2009) PMID: 19378138
    Egan M, Lee EK, Chiu JC, Coruzzi G, Desalle R
48. A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis.
    PLoS Comput Biol (2009 Mar) PMC2652106 free full-text archive
    Krouk G, Tranchina D, Lejay L, Cruikshank AA, Shasha D, Coruzzi GM, Gutierrez RA
49. 2020 vision for biology: the role of plants in addressing grand challenges in biology.
    Mol Plant (2008 Jul) PMID: 19825561
    Bender J, Benfey P, Bergmann D, Borevitz J, Coruzzi G, Dangl J, Dean C, Ecker J, Estelle M, Glazebrook J, Grant S, Guerinot ML, Gutierrez R, Long J, Nordborg M, Poethig S, Raikhel N, Schmitt J, Schnittger A, Vidal M
50. 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 Apr 4) PMC2335094 free full-text archive
    Thum KE, Shin MJ, Gutierrez RA, Mukherjee I, Katari MS, Nero D, Shasha D, Coruzzi GM
51. 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 Mar 25) PMC2290744 free full-text archive
    Gutierrez RA, Stokes TL, Thum K, Xu X, Obertello M, Katari MS, Tanurdzic M, Dean A, Nero DC, McClung CR, Coruzzi GM
52. Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics.
    BMC Bioinformatics (2008 Feb 19) PMC2270260 free full-text archive
    Sarkar IN, Egan MG, Coruzzi G, Lee EK, DeSalle R
53. Cell-specific nitrogen responses mediate developmental plasticity.
    Proc Natl Acad Sci U S A (2008 Jan 15) PMC2206617 free full-text archive
    Gifford ML, Dean A, Gutierrez RA, Coruzzi GM, Birnbaum KD
54. Insights into the genomic nitrate response using genetics and the Sungear Software System.
    J Exp Bot (2007) PMID: 17470441
    Gutierrez RA, Gifford ML, Poultney C, Wang R, Shasha DE, Coruzzi GM, Crawford NM
55. Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis.
    Genome Biol (2007) PMC1839130 free full-text archive
    Gutierrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM
56. Adaptive combinatorial design to explore large experimental spaces: approach and validation.
    Syst Biol (Stevenage) (2004 Dec) PMID: 17051692
    Lejay LV, Shasha DE, Palenchar PM, Kouranov AY, Cruikshank AA, Chou MF, Coruzzi GM
57. Sungear: interactive visualization and functional analysis of genomic datasets.
    Bioinformatics (2007 Jan 15) PMID: 17018536
    Poultney CS, Gutierrez RA, Katari MS, Gifford ML, Paley WB, Coruzzi GM, Shasha DE
58. ESTimating plant phylogeny: lessons from partitioning.
    BMC Evol Biol (2006 Jun 15) PMC1564041 free full-text archive
    de la Torre JE, Egan MG, Katari MS, Brenner ED, Stevenson DW, Coruzzi GM, DeSalle R
59. OrthologID: automation of genome-scale ortholog identification within a parsimony framework.
    Bioinformatics (2006 Mar 15) PMID: 16410324
    Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R
60. EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes.
    BMC Genomics (2005 Oct 15) PMC1285361 free full-text archive
    Brenner ED, Katari MS, Stevenson DW, Rudd SA, Douglas AW, Moss WN, Twigg RW, Runko SJ, Stellari GM, McCombie WR, Coruzzi GM
61. Systems biology for the virtual plant.
    Plant Physiol (2005 Jun) PMC1150368 free full-text archive
    Gutierrez RA, Shasha DE, Coruzzi GM
62. 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) PMC545782 free full-text archive
    Palenchar PM, Kouranov A, Lejay LV, Coruzzi GM
63. Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis.
    Plant Physiol (2004 Sep) PMC523318 free full-text archive
    Wang R, Tischner R, Gutierrez RA, Hoffman M, Xing X, Chen M, Coruzzi G, Crawford NM
64. Genome-wide investigation of light and carbon signaling interactions in Arabidopsis.
    Genome Biol (2004) PMC395748 free full-text archive
    Thum KE, Shin MJ, Palenchar PM, Kouranov A, Coruzzi GM
65. Correlation of ASN2 gene expression with ammonium metabolism in Arabidopsis.
    Plant Physiol (2004 Jan) PMC316312 free full-text archive
    Wong HK, Chan HK, Coruzzi GM, Lam HM
66. Expressed sequence tag analysis in Cycas, the most primitive living seed plant.
    Genome Biol (2003) PMC329417 free full-text archive
    Brenner ED, Stevenson DW, McCombie RW, Katari MS, Rudd SA, Mayer KF, Palenchar PM, Runko SJ, Twigg RW, Dai G, Martienssen RA, Benfey PN, Coruzzi GM
67. Achieving the in silico plant. Systems biology and the future of plant biological research.
    Plant Physiol (2003 Jun) PMC1540317 free full-text archive
    Raikhel NV, Coruzzi GM
68. Overexpression of the ASN1 gene enhances nitrogen status in seeds of Arabidopsis.
    Plant Physiol (2003 Jun) PMC167031 free full-text archive
    Lam HM, Wong P, Chan HK, Yam KM, Chen L, Chow CM, Coruzzi GM
69. Light- and carbon-signaling pathways. Modeling circuits of interactions.
    Plant Physiol (2003 Jun) PMC166987 free full-text archive
    Thum KE, Shasha DE, Lejay LV, Coruzzi GM
70. Overexpression of cytosolic glutamine synthetase. Relation to nitrogen, light, and photorespiration.
    Plant Physiol (2002 Jul) PMC166511 free full-text archive
    Oliveira IC, Brears T, Knight TJ, Clark A, Coruzzi GM
71. Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana.
    Mol Biol Evol (2002 Jul) PMID: 12082126
    Chiu JC, Brenner ED, DeSalle R, Nitabach MN, Holmes TC, Coruzzi GM
72. Molecular and physiological analysis of Arabidopsis mutants defective in cytosolic or chloroplastic aspartate aminotransferase.
    Plant Physiol (2002 Jun) PMC161691 free full-text archive
    Miesak BH, Coruzzi GM
73. Arabidopsis glt1-T mutant defines a role for NADH-GOGAT in the non-photorespiratory ammonium assimilatory pathway.
    Plant J (2002 Feb) PMID: 11844111
    Lancien M, Martin M, Hsieh MH, Leustek T, Goodman H, Coruzzi GM
74. Using combinatorial design to study regulation by multiple input signals. A tool for parsimony in the post-genomics era.
    Plant Physiol (2001 Dec) PMC1540192 free full-text archive
    Shasha DE, Kouranov AY, Lejay LV, Chou MF, Coruzzi GM
75. The identity of plant glutamate receptors.
    Science (2001 May 25) PMID: 11379626
    Lacombe B, Becker D, Hedrich R, DeSalle R, Hollmann M, Kwak JM, Schroeder JI, Le Novere N, Nam HG, Spalding EP, Tester M, Turano FJ, Chiu J, Coruzzi G
76. Metabolite and light regulation of metabolism in plants: lessons from the study of a single biochemical pathway.
    Braz J Med Biol Res (2001 May) PMID: 11323742
    Oliveira IC, Brenner E, Chiu J, Hsieh MH, Kouranov A, Lam HM, Shin MJ, Coruzzi G
77. Carbon and nitrogen sensing and signaling in plants: emerging 'matrix effects'.
    Curr Opin Plant Biol (2001 Jun) PMID: 11312136
    Coruzzi GM, Zhou L
78. Nitrogen and carbon nutrient and metabolite signaling in plants.
    Plant Physiol (2001 Jan) PMC1539326 free full-text archive
    Coruzzi G, Bush DR
79. Arabidopsis mutants resistant to S(+)-beta-methyl-alpha, beta-diaminopropionic acid, a cycad-derived glutamate receptor agonist.
    Plant Physiol (2000 Dec) PMC59860 free full-text archive
    Brenner ED, Martinez‑Barboza N, Clark AP, Liang QS, Stevenson DW, Coruzzi GM
80. 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 Jun) PMC1539254 free full-text archive
    Chory J, Ecker JR, Briggs S, Caboche M, Coruzzi GM, Cook D, Dangl J, Grant S, Guerinot ML, Henikoff S, Martienssen R, Okada K, Raikhel NV, Somerville CR, Weigel D
81. Carbon and amino acids reciprocally modulate the expression of glutamine synthetase in Arabidopsis.
    Plant Physiol (1999 Sep) PMC59385 free full-text archive
    Oliveira IC, Coruzzi GM
82. Molecular evolution of glutamate receptors: a primitive signaling mechanism that existed before plants and animals diverged.
    Mol Biol Evol (1999 Jun) PMID: 10368960
    Chiu J, DeSalle R, Lam HM, Meisel L, Coruzzi G
83. Reciprocal regulation of distinct asparagine synthetase genes by light and metabolites in Arabidopsis thaliana.
    Plant J (1998 Nov) PMID: 9881155
    Lam HM, Hsieh MH, Coruzzi G
84. Glutamate-receptor genes in plants.
    Nature (1998 Nov 12) PMID: 9823891
    Lam HM, Chiu J, Hsieh MH, Meisel L, Oliveira IC, Shin M, Coruzzi G
85. A PII-like protein in Arabidopsis: putative role in nitrogen sensing.
    Proc Natl Acad Sci U S A (1998 Nov 10) PMC24990 free full-text archive
    Hsieh MH, Lam HM, van de Loo FJ, Coruzzi G
86. Arabidopsis mutants define an in vivo role for isoenzymes of aspartate aminotransferase in plant nitrogen assimilation.
    Genetics (1998 Jun) PMC1460188 free full-text archive
    Schultz CJ, Hsu M, Miesak B, Coruzzi GM
87. Arabidopsis gls mutants and distinct Fd-GOGAT genes. Implications for photorespiration and primary nitrogen assimilation.
    Plant Cell (1998 May) PMC144371 free full-text archive
    Coschigano KT, Melo‑Oliveira R, Lim J, Coruzzi GM
88. Light-induced transcriptional repression of the pea AS1 gene: identification of cis-elements and transfactors.
    Plant J (1997 Nov) PMID: 9418044
    Ngai N, Tsai FY, Coruzzi G
89. THE MOLECULAR-GENETICS OF NITROGEN ASSIMILATION INTO AMINO ACIDS IN HIGHER PLANTS.
    Annu Rev Plant Physiol Plant Mol Biol (1996 Jun) PMID: 15012301
    Lam HM, Coschigano KT, Oliveira IC, Melo‑Oliveira R, Coruzzi GM
90. Arabidopsis mutant analysis and gene regulation define a nonredundant role for glutamate dehydrogenase in nitrogen assimilation.
    Proc Natl Acad Sci U S A (1996 May 14) PMC39345 free full-text archive
    Melo‑Oliveira R, Oliveira IC, Coruzzi GM
91. Molecular evolution of duplicate copies of genes encoding cytosolic glutamine synthetase in Pisum sativum.
    Plant Mol Biol (1995 Dec) PMID: 8616212
    Walker EL, Weeden NF, Taylor CB, Green P, Coruzzi GM
92. Use of Arabidopsis mutants and genes to study amide amino acid biosynthesis.
    Plant Cell (1995 Jul) PMC160882 free full-text archive
    Lam HM, Coschigano K, Schultz C, Melo‑Oliveira R, Tjaden G, Oliveira I, Ngai N, Hsieh MH, Coruzzi G
93. Cis elements and trans-acting factors affecting regulation of a nonphotosynthetic light-regulated gene for chloroplast glutamine synthetase.
    Plant Physiol (1995 Jul) PMC157463 free full-text archive
    Tjaden G, Edwards JW, Coruzzi GM
94. The aspartate aminotransferase gene family of Arabidopsis encodes isoenzymes localized to three distinct subcellular compartments.
    Plant J (1995 Jan) PMID: 7894512
    Schultz CJ, Coruzzi GM
95. Metabolic regulation of the gene encoding glutamine-dependent asparagine synthetase in Arabidopsis thaliana.
    Plant Physiol (1994 Dec) PMC159672 free full-text archive
    Lam HM, Peng SS, Coruzzi GM
96. A novel AT-rich DNA binding protein that combines an HMG I-like DNA binding domain with a putative transcription domain.
    Plant Cell (1994 Jan) PMC160420 free full-text archive
    Tjaden G, Coruzzi GM
97. Ectopic Overexpression of Asparagine Synthetase in Transgenic Tobacco.
    Plant Physiol (1993 Dec) PMC159117 free full-text archive
    Brears T, Liu C, Knight TJ, Coruzzi GM
98. A Crucial Role for the NSF Postdoctoral Fellowship Program in Plant Biology.
    Plant Cell (1993 Jul) PMC160310 free full-text archive
    Coruzzi GM, Last RL
99. A gene network controlling glutamine and asparagine biosynthesis in plants.
    Plant J (1991 Nov) PMID: 1688250
    McGrath RB, Coruzzi GM
100. Light represses transcription of asparagine synthetase genes in photosynthetic and nonphotosynthetic organs of plants.
     Mol Cell Biol (1991 Oct) PMC361478 free full-text archive
     Tsai FY, Coruzzi G
101. 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 Sep) PMID: 1688248
     Brears T, Walker EL, Coruzzi GM
102. Cell-specific expression in transgenic plants reveals nonoverlapping roles for chloroplast and cytosolic glutamine synthetase.
     Proc Natl Acad Sci U S A (1990 May) PMC53920 free full-text archive
     Edwards JW, Walker EL, Coruzzi GM
103. Dark-induced and organ-specific expression of two asparagine synthetase genes in Pisum sativum.
     EMBO J (1990 Feb) PMC551669 free full-text archive
     Tsai FY, Coruzzi GM
104. Cell-specific gene expression in plants.
     Annu Rev Genet (1990) PMID: 2088170
     Edwards JW, Coruzzi GM
105. Developmentally Regulated Expression of the Gene Family for Cytosolic Glutamine Synthetase in Pisum sativum.
     Plant Physiol (1989 Oct) PMC1062059 free full-text archive
     Walker EL, Coruzzi GM
106. Photorespiration and light act in concert to regulate the expression of the nuclear gene for chloroplast glutamine synthetase.
     Plant Cell (1989 Feb) PMC159756 free full-text archive
     Edwards JW, Coruzzi GM
107. Chloroplast and cytosolic glutamine synthetase are encoded by homologous nuclear genes which are differentially expressed in vivo.
     J Biol Chem (1988 Jul 15) PMID: 2898472
     Tingey SV, Tsai FY, Edwards JW, Walker EL, Coruzzi GM
108. Glutamine Synthetase of Nicotiana plumbaginifolia: Cloning and in Vivo Expression.
     Plant Physiol (1987 Jun) PMC1056585 free full-text archive
     Tingey SV, Coruzzi GM
109. Glutamine synthetase genes of pea encode distinct polypeptides which are differentially expressed in leaves, roots and nodules.
     EMBO J (1987 Jan) PMC553348 free full-text archive
     Tingey SV, Walker EL, Coruzzi GM
110. Expression dynamics of the pea rbcS multigene family and organ distribution of the transcripts.
     EMBO J (1986 Sep) PMC1167083 free full-text archive
     Fluhr R, Moses P, Morelli G, Coruzzi G, Chua NH
111. Molecular biology of C4 photosynthesis in Zea mays: differential localization of proteins and mRNAs in the two leaf cell types.
     Plant Mol Biol (1984 Nov) PMID: 24310577
     Broglie R, Coruzzi G, Keith B, Chua NH
112. Tissue-specific and light-regulated expression of a pea nuclear gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase.
     EMBO J (1984 Aug) PMC557581 free full-text archive
     Coruzzi G, Broglie R, Edwards C, Chua NH
113. Light-regulated expression of a pea ribulose-1,5-bisphosphate carboxylase small subunit gene in transformed plant cells.
     Science (1984 May 25) PMID: 6719112
     Broglie R, Coruzzi G, Fraley RT, Rogers SG, Horsch RB, Niedermeyer JG, Fink CL, Chua NH
114. 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 Feb 10) PMID: 6296093
     Coruzzi G, Broglie R, Cashmore A, Chua NH
115. 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 Dec 25) PMID: 7031051
     Coruzzi G, Bonitz SG, Thalenfeld BE, Tzagoloff A
116. 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 Dec 25) PMID: 6254986
     Bonitz SG, Coruzzi G, Thalenfeld BE, Tzagoloff A, Macino G
117. Assembly of the mitochondrial membrane system. Physical map of the Oxi3 locus of yeast mitochondrial DNA.
     J Biol Chem (1980 Dec 25) PMID: 6254985
     Bonitz SG, Coruzzi G, Thalenfeld BE, Tzagoloff A, Macino G
118. Transfer RNA genes in the cap-oxil region of yeast mitochondrial DNA.
     Nucleic Acids Res (1980 Nov 11) PMC324276 free full-text archive
     Berlani RE, Bonitz SG, Coruzzi G, Nobrega M, Tzagoloff A
119. Codon recognition rules in yeast mitochondria.
     Proc Natl Acad Sci U S A (1980 Jun) PMC349575 free full-text archive
     Bonitz SG, Berlani R, Coruzzi G, Li M, Macino G, Nobrega FG, Nobrega MP, Thalenfeld BE, Tzagoloff A
120. Assembly of the mitochondrial membrane system. DNA sequence of subunit 2 of yeast cytochrome oxidase.
     J Biol Chem (1979 Sep 25) PMID: 225327
     Coruzzi G, Tzagoloff A
121. Use of the UGA terminator as a tryptophan codon in yeast mitochondria.
     Proc Natl Acad Sci U S A (1979 Aug) PMC383918 free full-text archive
     Macino G, Coruzzi G, Nobrega FG, Li M, Tzagoloff A
122. Assembly of the mitochondrial membrane system: mutations in the pho2 locus of the mitochondrial genome of Saccharomyces cerevisiae.
     Eur J Biochem (1978 Dec 1) PMID: 153229
     Coruzzi G, Trembath MK, Tzagoloff A