PubMed

The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.

de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R.

PLoS One. 2009 Jun 2;4(6):e5764.PMID: 19503618 [PubMed - indexed for MEDLINE]Related articlesFree article

A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule".

Nero D, Krouk G, Tranchina D, Coruzzi GM.

BMC Syst Biol. 2009 Jun 6;3:59.PMID: 19500399 [PubMed - indexed for MEDLINE]Related articlesFree article

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.

Brenner ED, Feinberg P, Runko S, Coruzzi GM.

Plant Mol Biol. 2009 Jul;70(5):523-33. Epub 2009 May 2.PMID: 19412571 [PubMed - indexed for MEDLINE]Related articles

Gene orthology assessment with OrthologID.

Egan M, Lee EK, Chiu JC, Coruzzi G, Desalle R.

Methods Mol Biol. 2009;537:23-38.PMID: 19378138 [PubMed - indexed for MEDLINE]Related articles

A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis.

Krouk G, Tranchina D, Lejay L, Cruikshank AA, Shasha D, Coruzzi GM, Gutiérrez RA.

PLoS Comput Biol. 2009 Mar;5(3):e1000326. Epub 2009 Mar 20.PMID: 19300494 [PubMed - indexed for MEDLINE]Related articlesFree article

An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis.

Thum KE, Shin MJ, Gutiérrez RA, Mukherjee I, Katari MS, Nero D, Shasha D, Coruzzi GM.

BMC Syst Biol. 2008 Apr 4;2:31.PMID: 18387196 [PubMed - indexed for MEDLINE]Related articlesFree article

Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1.

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

Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4939-44. Epub 2008 Mar 14.PMID: 18344319 [PubMed - indexed for MEDLINE]Related articlesFree article

Cell-specific nitrogen responses mediate developmental plasticity.

Gifford ML, Dean A, Gutierrez RA, Coruzzi GM, Birnbaum KD.

Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):803-8. Epub 2008 Jan 7.PMID: 18180456 [PubMed - indexed for MEDLINE]Related articlesFree article

Insights into the genomic nitrate response using genetics and the Sungear Software System.

Gutiérrez RA, Gifford ML, Poultney C, Wang R, Shasha DE, Coruzzi GM, Crawford NM.

J Exp Bot. 2007;58(9):2359-67. Epub 2007 Apr 29. Review.PMID: 17470441 [PubMed - indexed for MEDLINE]Related articlesFree article

Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis.

Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM.

Genome Biol. 2007;8(1):R7.PMID: 17217541 [PubMed - indexed for MEDLINE]Related articlesFree article

Adaptive combinatorial design to explore large experimental spaces: approach and validation.

Lejay LV, Shasha DE, Palenchar PM, Kouranov AY, Cruikshank AA, Chou MF, Coruzzi GM.

Syst Biol (Stevenage). 2004 Dec;1(2):206-12.PMID: 17051692 [PubMed - indexed for MEDLINE]Related articles

Sungear: interactive visualization and functional analysis of genomic datasets.

Poultney CS, Gutiérrez RA, Katari MS, Gifford ML, Paley WB, Coruzzi GM, Shasha DE.

Bioinformatics. 2007 Jan 15;23(2):259-61. Epub 2006 Oct 2.PMID: 17018536 [PubMed - indexed for MEDLINE]Related articlesFree article

ESTimating plant phylogeny: lessons from partitioning.

de la Torre JE, Egan MG, Katari MS, Brenner ED, Stevenson DW, Coruzzi GM, DeSalle R.

BMC Evol Biol. 2006 Jun 15;6:48.PMID: 16776834 [PubMed - indexed for MEDLINE]Related articlesFree article

OrthologID: automation of genome-scale ortholog identification within a parsimony framework.

Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R.

Bioinformatics. 2006 Mar 15;22(6):699-707. Epub 2006 Jan 12.PMID: 16410324 [PubMed - indexed for MEDLINE]Related articlesFree article

EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes.

Brenner ED, Katari MS, Stevenson DW, Rudd SA, Douglas AW, Moss WN, Twigg RW, Runko SJ, Stellari GM, McCombie WR, Coruzzi GM.

BMC Genomics. 2005 Oct 15;6:143.PMID: 16225698 [PubMed - indexed for MEDLINE]Related articlesFree article

Systems biology for the virtual plant.

Gutiérrez RA, Shasha DE, Coruzzi GM.

Plant Physiol. 2005 Jun;138(2):550-4. Review. No abstract available. PMID: 15955912 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants.

Palenchar PM, Kouranov A, Lejay LV, Coruzzi GM.

Genome Biol. 2004;5(11):R91. Epub 2004 Oct 29.PMID: 15535867 [PubMed - indexed for MEDLINE]Related articlesFree article

Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis.

Wang R, Tischner R, Gutiérrez RA, Hoffman M, Xing X, Chen M, Coruzzi G, Crawford NM.

Plant Physiol. 2004 Sep;136(1):2512-22. Epub 2004 Aug 27.PMID: 15333754 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide investigation of light and carbon signaling interactions in Arabidopsis.

Thum KE, Shin MJ, Palenchar PM, Kouranov A, Coruzzi GM.

Genome Biol. 2004;5(2):R10. Epub 2004 Jan 27.PMID: 14759260 [PubMed - indexed for MEDLINE]Related articlesFree article

Correlation of ASN2 gene expression with ammonium metabolism in Arabidopsis.

Wong HK, Chan HK, Coruzzi GM, Lam HM.

Plant Physiol. 2004 Jan;134(1):332-8. Epub 2003 Dec 11.PMID: 14671018 [PubMed - indexed for MEDLINE]Related articlesFree article