 |
Carroll and Milton Petrie Professor; Professor of Biology; Chair, Department of Biology
Ph.D.-M.S. 1979 (Molecular and Cell Biology), New York University; B.S. 1976 (Biology), Fordham.
Office Address:
| New York University |
| Center for Genomics and Systems Biology |
| Department of Biology |
| 1009 Silver Center |
| 100 Washington Square East |
| New York, NY 10003-6688 |
Email:
Phone: (212) 998-3963
Fax: (212) 995-4015
List of Publications from Pubmed
Lab Homepage
Curriculum Vitae
Download Sample Publications (PDFs)
|
Research
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:
- 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.
- 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).
- 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
FUNDING:
NIH NIGMS GRANT GM32877: "Regulation of amino acid biosynthesis genes in plants"
P.I.: Gloria Coruzzi
NSF Arabidopsis 2010 Genome Grant (IBN0115586):"N2010:
Nitrogen Networks in Plants" P.I. Gloria Coruzzi, Co-PIs; D. Shasha
(NYU Courant), N.Crawford (UCSD), Ken Birnbaum (NYU Center for
Comparative Functional Genomics).
NSF Plant Genome Grant: DBI-0421604. "Genomics of Comparative Seed Evolution" P.I.: Gloria Coruzzi; Co-PIs: Stevenson (NYBG), McCombie (CSHL), DeSalle (AMNH).
NSF Database Activities:
DBI-0445666, "Conceptual Data Integration for the Virtual Plant".
Coruzzi , PI, CoPIs: Gutierrez R (U Catolica de Chile), Shasha D (NYU
Courant).
DOE GRANT DEFG02-89ER14034: "Asparagine synthetase gene regulation and plant nitrogen metabolism" P.I. Coruzzi
COLLABORATORS:
VirtualPlant Project
Dr. Rodrigo Gutierrez (Catholical U, Chile)
Dr. Manpreet Katari (NYU Biology/Coruzzi lab)
Chris Poultney (NYU Courant)
Dr. Dennis Shasha (NYU, Courant Institute of Math & Computer Science)
N-network projects
Dr. Ken Birnbaum (NYU Center for Comparative Functional Genomics)
Dr. Francesca Chiaromonte (NYU Courant/Biology)
Dr. Nigel Crawford (UCSD)
Dr. Rodrigo Gutierrez (U Catolica de Chile)
Dr. Hon-Ming Lam (Chinese University of Hong Kong)
Dr. Dan Tranchina (NYU Courant)
Comparative Genomics of Seed Evolution
Dr. Eric Brenner (NYBG)
Dr. Rob DeSalle (American Museum of Natural History)
Dr. Rob Martienssen (CSHL)
Dr. Richard McCombie (CSHL)
Dr. Dennis Stevenson (New York Botanical Garden)
Biosketch
Gloria Coruzzi is currently the Carroll & Milton Petrie Professor
and Chair 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 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
currently 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 AAAS
Fellow in 2005 and currently serves on numerous science advisory and
editorial boards.
Teaching Activities
I have been involved in developing a specialized graduate training
track that concerns the molecular evolution of plants and animals
called BRIDGES: Biotic Resources: Integrating Development, Genetics,
Evolution and Systematics which is currently run by Dr. David Fitch.
The BRIDGES PhD track was developed jointly by NYU faculty and faculty
the New York Botanical Garden (NYBG) and the American Museum of Natural
History (AMNH). I teach in the following undergradiate and graduate
courses: V23.0012 Principles of Biology II, V230014 Honors Principles
of Biology II, V23.0022 Molecular and Cellular Biology; G23.1072
Molecular Controls of Organism Form and Function, G23.1128 Genomics;
G23.1002/2004 BioCore II & IV: Genes, Systems and Evolution.
Laboratory Members
See Coruzzi Laboratory Webpage for more information on people & projects.
Current Laboratory Members
Gloria Coruzzi: gloria.coruzzi@nyu.edu
Post doctoral Fellows
Miriam Gifford: Miriam.gifford@nyu.edu
Manpreet Katari: mkatari@nyu.edu
Mariana Obertello: mo47@nyu.edu
Karen Thum: ket2@nyu.edu
Graduate Students
Eduardo dela Torre: jdl266@nyu.edu
Philip Feinberg: pbf220@nyu.edu
Damion Nero: damion643@aol.com
Research Assistants
Alexis Cruikshank: ac92@nyu.edu
Alexis Dean: ad834@nyu.edu
Suzan Runko: sjr0891@nyu.edu
Areas of Research/Interest
Plant Systems Biology and Evolutionary Genomics
External Affiliations
Editorial Board; Current Opinions in Plant Biology, 1998-present; Board of Directors, International Society of Plant Molecular Biology, 1996-1999; New York Botanical Garden, Advisory Committee for Systematic Botany, 1995-present; Board Member, North American Arabidopsis Steering Committee, 1994-1997; Associate Editor, Plant Physiology, 1992-1998.
Fellowships/Honors
AAAS Fellow, 2005; Carroll and Milton Petrie Chair in Biology, NYU 1996- present; National Institutes of Health Grant, GM32877, 1996-2000; National Science Foundation Grant, MCB93-04913, 1996-1999; United States Department of Energy Grant, DEFG0292ER20071, 1995-1998; Herbert and Margaret Sokol Award in the Sciences, NYU Dec. 1996.
