Plant Systems Biology @ The Coruzzi Laboratory

The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.
PLoS One (2009)
de la Torre-Barcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R

A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule".
BMC Syst Biol (2009)
Nero D, Krouk G, Tranchina D, 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 Jul)
Brenner ED, Feinberg P, Runko S, Coruzzi GM

Gene orthology assessment with OrthologID.
Methods Mol Biol (2009)
Egan M, Lee EK, Chiu JC, Coruzzi G, Desalle R

A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis.
PLoS Comput Biol (2009 Mar)
Krouk G, Tranchina D, Lejay L, Cruikshank AA, Shasha D, Coruzzi GM, Gutierrez RA

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)
Thum KE, Shin MJ, Gutierrez RA, Mukherjee I, Katari MS, Nero D, Shasha D, Coruzzi GM

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)
Gutierrez RA, Stokes TL, Thum K, Xu X, Obertello M, Katari MS, Tanurdzic M, Dean A, Nero DC, McClung CR, Coruzzi GM

Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics.
BMC Bioinformatics (2008)
Sarkar IN, Egan MG, Coruzzi G, Lee EK, DeSalle R

Cell-specific nitrogen responses mediate developmental plasticity.
Proc Natl Acad Sci U S A (2008 Jan 15)
Gifford ML, Dean A, Gutierrez RA, Coruzzi GM, Birnbaum KD

Insights into the genomic nitrate response using genetics and the Sungear Software System.
J Exp Bot (2007)
Gutierrez RA, Gifford ML, Poultney C, Wang R, Shasha DE, Coruzzi GM, Crawford NM

Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis.
Genome Biol (2007)
Gutierrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM

Adaptive combinatorial design to explore large experimental spaces: approach and validation.
Syst Biol (Stevenage) (2004 Dec)
Lejay LV, Shasha DE, Palenchar PM, Kouranov AY, Cruikshank AA, Chou MF, Coruzzi GM

Sungear: interactive visualization and functional analysis of genomic datasets.
Bioinformatics (2007 Jan 15)
Poultney CS, Gutierrez RA, Katari MS, Gifford ML, Paley WB, Coruzzi GM, Shasha DE

ESTimating plant phylogeny: lessons from partitioning.
BMC Evol Biol (2006)
de la Torre JE, Egan MG, Katari MS, Brenner ED, Stevenson DW, Coruzzi GM, DeSalle R

OrthologID: automation of genome-scale ortholog identification within a parsimony framework.
Bioinformatics (2006 Mar 15)
Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R

EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes.
BMC Genomics (2005)
Brenner ED, Katari MS, Stevenson DW, Rudd SA, Douglas AW, Moss WN, Twigg RW, Runko SJ, Stellari GM, McCombie WR, Coruzzi GM

Systems biology for the virtual plant.
Plant Physiol (2005 Jun)
Gutierrez RA, Shasha DE, 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)
Palenchar PM, Kouranov A, Lejay LV, Coruzzi GM

Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis.
Plant Physiol (2004 Sep)
Wang R, Tischner R, Gutierrez RA, Hoffman M, Xing X, Chen M, Coruzzi G, Crawford NM

Genome-wide investigation of light and carbon signaling interactions in Arabidopsis.
Genome Biol (2004)
Thum KE, Shin MJ, Palenchar PM, Kouranov A, Coruzzi GM

Correlation of ASN2 gene expression with ammonium metabolism in Arabidopsis.
Plant Physiol (2004 Jan)
Wong HK, Chan HK, Coruzzi GM, Lam HM

Expressed sequence tag analysis in Cycas, the most primitive living seed plant.
Genome Biol (2003)
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

Achieving the in silico plant. Systems biology and the future of plant biological research.
Plant Physiol (2003 Jun)
Raikhel NV, Coruzzi GM

Overexpression of the ASN1 gene enhances nitrogen status in seeds of Arabidopsis.
Plant Physiol (2003 Jun)
Lam HM, Wong P, Chan HK, Yam KM, Chen L, Chow CM, Coruzzi GM

Light- and carbon-signaling pathways. Modeling circuits of interactions.
Plant Physiol (2003 Jun)
Thum KE, Shasha DE, Lejay LV, Coruzzi GM

Overexpression of cytosolic glutamine synthetase. Relation to nitrogen, light, and photorespiration.
Plant Physiol (2002 Jul)
Oliveira IC, Brears T, Knight TJ, Clark A, Coruzzi GM

Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana.
Mol Biol Evol (2002 Jul)
Chiu JC, Brenner ED, DeSalle R, Nitabach MN, Holmes TC, Coruzzi GM

Molecular and physiological analysis of Arabidopsis mutants defective in cytosolic or chloroplastic aspartate aminotransferase.
Plant Physiol (2002 Jun)
Miesak BH, Coruzzi GM

Arabidopsis glt1-T mutant defines a role for NADH-GOGAT in the non-photorespiratory ammonium assimilatory pathway.
Plant J (2002 Feb)
Lancien M, Martin M, Hsieh MH, Leustek T, Goodman H, Coruzzi GM

Using combinatorial design to study regulation by multiple input signals. A tool for parsimony in the post-genomics era.
Plant Physiol (2001 Dec)
Shasha DE, Kouranov AY, Lejay LV, Chou MF, Coruzzi GM

The identity of plant glutamate receptors.
Science (2001 May 25)
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

Metabolite and light regulation of metabolism in plants: lessons from the study of a single biochemical pathway.
Braz J Med Biol Res (2001 May)
Oliveira IC, Brenner E, Chiu J, Hsieh MH, Kouranov A, Lam HM, Shin MJ, Coruzzi G

Carbon and nitrogen sensing and signaling in plants: emerging 'matrix effects'.
Curr Opin Plant Biol (2001 Jun)
Coruzzi GM, Zhou L

Nitrogen and carbon nutrient and metabolite signaling in plants.
Plant Physiol (2001 Jan)
Coruzzi G, Bush DR

Arabidopsis mutants resistant to S(+)-beta-methyl-alpha, beta-diaminopropionic acid, a cycad-derived glutamate receptor agonist.
Plant Physiol (2000 Dec)
Brenner ED, Martinez-Barboza N, Clark AP, Liang QS, Stevenson DW, Coruzzi GM

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)
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

Carbon and amino acids reciprocally modulate the expression of glutamine synthetase in Arabidopsis.
Plant Physiol (1999 Sep)
Oliveira IC, Coruzzi GM

Molecular evolution of glutamate receptors: a primitive signaling mechanism that existed before plants and animals diverged.
Mol Biol Evol (1999 Jun)
Chiu J, DeSalle R, Lam HM, Meisel L, Coruzzi G

Reciprocal regulation of distinct asparagine synthetase genes by light and metabolites in Arabidopsis thaliana.
Plant J (1998 Nov)
Lam HM, Hsieh MH, Coruzzi G

Glutamate-receptor genes in plants.
Nature (1998 Nov 12)
Lam HM, Chiu J, Hsieh MH, Meisel L, Oliveira IC, Shin M, Coruzzi G

A PII-like protein in Arabidopsis: putative role in nitrogen sensing.
Proc Natl Acad Sci U S A (1998 Nov 10)
Hsieh MH, Lam HM, van de Loo FJ, Coruzzi G

Arabidopsis mutants define an in vivo role for isoenzymes of aspartate aminotransferase in plant nitrogen assimilation.
Genetics (1998 Jun)
Schultz CJ, Hsu M, Miesak B, Coruzzi GM

Arabidopsis gls mutants and distinct Fd-GOGAT genes. Implications for photorespiration and primary nitrogen assimilation.
Plant Cell (1998 May)
Coschigano KT, Melo-Oliveira R, Lim J, Coruzzi GM

Light-induced transcriptional repression of the pea AS1 gene: identification of cis-elements and transfactors.
Plant J (1997 Nov)
Ngai N, Tsai FY, Coruzzi G

THE MOLECULAR-GENETICS OF NITROGEN ASSIMILATION INTO AMINO ACIDS IN HIGHER PLANTS.
Annu Rev Plant Physiol Plant Mol Biol (1996 Jun)
Lam HM, Coschigano KT, Oliveira IC, Melo-Oliveira R, 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 May 14)
Melo-Oliveira R, Oliveira IC, Coruzzi GM

Molecular evolution of duplicate copies of genes encoding cytosolic glutamine synthetase in Pisum sativum.
Plant Mol Biol (1995 Dec)
Walker EL, Weeden NF, Taylor CB, Green P, Coruzzi GM

Use of Arabidopsis mutants and genes to study amide amino acid biosynthesis.
Plant Cell (1995 Jul)
Lam HM, Coschigano K, Schultz C, Melo-Oliveira R, Tjaden G, Oliveira I, Ngai N, Hsieh MH, Coruzzi G

Cis elements and trans-acting factors affecting regulation of a nonphotosynthetic light-regulated gene for chloroplast glutamine synthetase.
Plant Physiol (1995 Jul)
Tjaden G, Edwards JW, Coruzzi GM

The aspartate aminotransferase gene family of Arabidopsis encodes isoenzymes localized to three distinct subcellular compartments.
Plant J (1995 Jan)
Schultz CJ, Coruzzi GM

Metabolic regulation of the gene encoding glutamine-dependent asparagine synthetase in Arabidopsis thaliana.
Plant Physiol (1994 Dec)
Lam HM, Peng SS, 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 Jan)
Tjaden G, Coruzzi GM

Ectopic Overexpression of Asparagine Synthetase in Transgenic Tobacco.
Plant Physiol (1993 Dec)
Brears T, Liu C, Knight TJ, Coruzzi GM

A Crucial Role for the NSF Postdoctoral Fellowship Program in Plant Biology.
Plant Cell (1993 Jul)
Coruzzi GM, Last RL

A gene network controlling glutamine and asparagine biosynthesis in plants.
Plant J (1991 Nov)
McGrath RB, Coruzzi GM

Light represses transcription of asparagine synthetase genes in photosynthetic and nonphotosynthetic organs of plants.
Mol Cell Biol (1991 Oct)
Tsai FY, Coruzzi G

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)
Brears T, 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 May)
Edwards JW, Walker EL, Coruzzi GM

Dark-induced and organ-specific expression of two asparagine synthetase genes in Pisum sativum.
EMBO J (1990 Feb)
Tsai FY, Coruzzi GM

Cell-specific gene expression in plants.
Annu Rev Genet (1990)
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 Feb)
Edwards JW, Coruzzi GM

Chloroplast and cytosolic glutamine synthetase are encoded by homologous nuclear genes which are differentially expressed in vivo.
J Biol Chem (1988 Jul 15)
Tingey SV, Tsai FY, Edwards JW, Walker EL, Coruzzi GM

Glutamine Synthetase of Nicotiana plumbaginifolia: Cloning and in Vivo Expression.
Plant Physiol (1987 Jun)
Tingey SV, Coruzzi GM

Glutamine synthetase genes of pea encode distinct polypeptides which are differentially expressed in leaves, roots and nodules.
EMBO J (1987 Jan)
Tingey SV, Walker EL, Coruzzi GM

Expression dynamics of the pea rbcS multigene family and organ distribution of the transcripts.
EMBO J (1986 Sep)
Fluhr R, Moses P, Morelli G, Coruzzi G, 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 Aug)
Coruzzi G, Broglie R, Edwards C, Chua NH

Light-regulated expression of a pea ribulose-1,5-bisphosphate carboxylase small subunit gene in transformed plant cells.
Science (1984 May 25)
Broglie R, Coruzzi G, Fraley RT, Rogers SG, Horsch RB, Niedermeyer JG, Fink CL, 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 Feb 10)
Coruzzi G, Broglie R, Cashmore A, Chua NH