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Publications

Plant Systems Biology @ The Coruzzi Lab

From predictive network modeling to trait evolution

 

  • Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution.
    PLoS Genet (2014 Jul)
    Delaux P, Varala K, Edger PP, Coruzzi GM, Pires JC, Ané J.

  • Finding a nitrogen niche: a systems integration of local and systemic nitrogen signalling in plants.
    J Exp Bot (2014 Oct)
    Li Y, Krouk G, Coruzzi GM, Ruffel S.

  • Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis.
    Proc Natl Acad Sci U S A (2014 Jul 15)
    Para A, Li Y, Marshall-Colón A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BOR, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM.

  • Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. Highly Accessed
    BMC Genomics (2013)
    Vidal EA, Moyano TC, Krouk G, Katari MS, Tanurdzic M, McCombie WR, Coruzzi GM, Gutiérrez RA.

  • A unified nomenclature of NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family members in plants.
    Trends Plant Sci (2014 Jan)
    Léran S, Varala K, Boyer J, Chiurazzi M, Crawford N, Daniel-Vedele F, David L, Dickstein R, Fernandez E, Forde B, Gassmann W, Geiger D, Gojon A, Gong J, Halkier BA, Harris JM, Hedrich R, Limami AM, Rentsch D, Seo M, Tsay Y, Zhang M, Coruzzi G, Lacombe B.

  • Plasticity regulators modulate specific root traits in discrete nitrogen environments.
    PLoS Genet (2013)
    Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD.

  • 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)
    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.

  • Gene regulatory networks in plants: learning causality from time and perturbation. Highly Accessed
    Genome Biol (2013)
    Krouk G, Lingeman J, Colon AM, Coruzzi G, Shasha D.

  • TARGET: a transient transformation system for genome-wide transcription factor target discovery.
    Mol Plant (2013 May)
    Bargmann BOR, Marshall-Colon A, Efroni I, Ruffel S, Birnbaum KD, Coruzzi GM, Krouk G.

  • RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis.
    Plant Physiol (2013 Mar)
    Ristova D, Rosas U, Krouk G, Ruffel S, Birnbaum KD, Coruzzi GM.

  • A functional phylogenomic view of the seed plants.
    PLoS Genet (2011 Dec)
    Lee EK, Cibrian-Jaramillo A, Kolokotronis S, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, Desalle R.

  • 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)
    Ruffel S, Krouk G, Ristova D, Shasha D, Birnbaum KD, Coruzzi GM.

  • 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)
    Widiez T, El Kafafi ES, Girin T, Berr A, Ruffel S, Krouk G, Vayssières A, Shen W, Coruzzi GM, Gojon A, Lepetit M.

  • A framework integrating plant growth with hormones and nutrients.
    Trends Plant Sci (2011 Apr)
    Krouk G, Ruffel S, Gutiérrez RA, Gojon A, Crawford NM, Coruzzi GM, Lacombe B.

  • Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate.
    Genome Biol (2010)
    Krouk G, Mirowski P, LeCun Y, Shasha DE, 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)
    Obertello M, Krouk G, Katari MS, Runko SJ, Coruzzi GM.

  • Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution.
    Genome Biol Evol (2010)
    Cibrián-Jaramillo A, De la Torre-Bárcena JE, Lee EK, Katari MS, Little DP, Stevenson DW, Martienssen R, Coruzzi GM, DeSalle R.

  • Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana.
    Proc Natl Acad Sci U S A (2010 Mar 2)
    Vidal EA, Araus V, Lu C, Parry G, Green PJ, Coruzzi GM, Gutiérrez RA.

  • Nitrate signaling: adaptation to fluctuating environments.
    Curr Opin Plant Biol (2010 Jun)
    Krouk G, Crawford NM, Coruzzi GM, Tsay Y.

  • In silico evaluation of predicted regulatory interactions in Arabidopsis thaliana.
    BMC Bioinformatics (2009)
    Nero D, Katari MS, Kelfer J, Tranchina D, Coruzzi GM.

  • VirtualPlant: a software platform to support systems biology research.
    Plant Physiol (2010 Feb)
    Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutiérrez RA.

  • A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling.
    Plant Physiol (2010 Feb)
    Ruffel S, Krouk G, Coruzzi GM.

  • The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.
    PLoS One (2009)
    de la Torre-Bárcena JE, Kolokotronis S, 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”. Highly Accessed
    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, Gutiérrez RA.

  • 2020 vision for biology: the role of plants in addressing grand challenges in biology.
    Mol Plant (2008 Jul)
    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.

  • An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. Highly Accessed
    BMC Syst Biol (2008)
    Thum KE, Shin MJ, Gutiérrez 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)
    Gutiérrez 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)
    Gutiérrez 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)
    Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM.

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

  • ESTimating plant phylogeny: lessons from partitioning. Highly Accessed
    BMC Evol Biol (2006)
    de la Torre JEB, 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.

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