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μChIP-Seq for Genome-Wide Mapping of In Vivo TF-DNA Interactions in Arabidopsis Root Protoplasts.

Para A, Li Y, Coruzzi GM.

Methods Mol Biol. 2018;1761:249-261. doi: 10.1007/978-1-4939-7747-5_19.


Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture.

Walker L, Boddington C, Jenkins D, Wang Y, Grønlund JT, Hulsmans J, Kumar S, Patel D, Moore JD, Carter A, Samavedam S, Bonomo G, Hersh DS, Coruzzi GM, Burroughs NJ, Gifford ML.

Plant Cell. 2017 Oct;29(10):2393-2412. doi: 10.1105/tpc.16.00961. Epub 2017 Sep 11.


Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root.

Ristova D, Carré C, Pervent M, Medici A, Kim GJ, Scalia D, Ruffel S, Birnbaum KD, Lacombe B, Busch W, Coruzzi GM, Krouk G.

Sci Signal. 2016 Oct 25;9(451):rs13.


A matter of time - How transient transcription factor interactions create dynamic gene regulatory networks.

Swift J, Coruzzi GM.

Biochim Biophys Acta. 2017 Jan;1860(1):75-83. doi: 10.1016/j.bbagrm.2016.08.007. Epub 2016 Aug 18. Review.


"Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run".

Doidy J, Li Y, Neymotin B, Edwards MB, Varala K, Gresham D, Coruzzi GM.

BMC Genomics. 2016 Feb 3;17:92. doi: 10.1186/s12864-016-2410-2.


Long-distance nitrate signaling displays cytokinin dependent and independent branches.

Ruffel S, Poitout A, Krouk G, Coruzzi GM, Lacombe B.

J Integr Plant Biol. 2016 Mar;58(3):226-9. doi: 10.1111/jipb.12453. Epub 2016 Feb 23.


"Hit-and-Run" leaves its mark: catalyst transcription factors and chromatin modification.

Varala K, Li Y, Marshall-Colón A, Para A, Coruzzi GM.

Bioessays. 2015 Aug;37(8):851-6. doi: 10.1002/bies.201400205. Epub 2015 Jun 23. Review.


From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks.

Li Y, Varala K, Coruzzi GM.

Trends Genet. 2015 Sep;31(9):509-15. doi: 10.1016/j.tig.2015.05.005. Epub 2015 Jun 10. Review.


Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice.

Obertello M, Shrivastava S, Katari MS, Coruzzi GM.

Plant Physiol. 2015 Aug;168(4):1830-43. doi: 10.1104/pp.114.255877. Epub 2015 Jun 4.


The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants.

Li Y, Mukherjee I, Thum KE, Tanurdzic M, Katari MS, Obertello M, Edwards MB, McCombie WR, Martienssen RA, Coruzzi GM.

Genome Biol. 2015 Apr 19;16:79. doi: 10.1186/s13059-015-0640-2.


AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip.

Medici A, Marshall-Colon A, Ronzier E, Szponarski W, Wang R, Gojon A, Crawford NM, Ruffel S, Coruzzi GM, Krouk G.

Nat Commun. 2015 Feb 27;6:6274. doi: 10.1038/ncomms7274.


Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution.

Delaux PM, Varala K, Edger PP, Coruzzi GM, Pires JC, Ané JM.

PLoS Genet. 2014 Jul 17;10(7):e1004487. doi: 10.1371/journal.pgen.1004487. eCollection 2014 Jul.


Finding a nitrogen niche: a systems integration of local and systemic nitrogen signalling in plants.

Li Y, Krouk G, Coruzzi GM, Ruffel S.

J Exp Bot. 2014 Oct;65(19):5601-10. doi: 10.1093/jxb/eru263. Epub 2014 Jun 24. Review.


Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis.

Para A, Li Y, Marshall-Colón A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM.

Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10371-6. doi: 10.1073/pnas.1404657111. Epub 2014 Jun 23.


Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots.

Vidal EA, Moyano TC, Krouk G, Katari MS, Tanurdzic M, McCombie WR, Coruzzi GM, Gutiérrez RA.

BMC Genomics. 2013 Oct 11;14:701. doi: 10.1186/1471-2164-14-701.


Plasticity regulators modulate specific root traits in discrete nitrogen environments.

Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD.

PLoS Genet. 2013;9(9):e1003760. doi: 10.1371/journal.pgen.1003760. Epub 2013 Sep 5.


Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture.

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.

Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):15133-8. doi: 10.1073/pnas.1305883110. Epub 2013 Aug 26. Erratum in: Proc Natl Acad Sci U S A. 2015 May 12;112(19):E2555.


TARGET: a transient transformation system for genome-wide transcription factor target discovery.

Bargmann BO, Marshall-Colon A, Efroni I, Ruffel S, Birnbaum KD, Coruzzi GM, Krouk G.

Mol Plant. 2013 May;6(3):978-80. doi: 10.1093/mp/sst010. Epub 2013 Jan 18. No abstract available.


RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis.

Ristova D, Rosas U, Krouk G, Ruffel S, Birnbaum KD, Coruzzi GM.

Plant Physiol. 2013 Mar;161(3):1086-96. doi: 10.1104/pp.112.210872. Epub 2013 Jan 18.


Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand.

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

Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18524-9. doi: 10.1073/pnas.1108684108. Epub 2011 Oct 24.


High nitrogen insensitive 9 (HNI9)-mediated systemic repression of root NO3- uptake is associated with changes in histone methylation.

Widiez T, El Kafafi el S, Girin T, Berr A, Ruffel S, Krouk G, Vayssières A, Shen WH, Coruzzi GM, Gojon A, Lepetit M.

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13329-34. doi: 10.1073/pnas.1017863108. Epub 2011 Jul 25.


A framework integrating plant growth with hormones and nutrients.

Krouk G, Ruffel S, Gutiérrez RA, Gojon A, Crawford NM, Coruzzi GM, Lacombe B.

Trends Plant Sci. 2011 Apr;16(4):178-82. doi: 10.1016/j.tplants.2011.02.004. Epub 2011 Mar 9.


Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate.

Krouk G, Mirowski P, LeCun Y, Shasha DE, Coruzzi GM.

Genome Biol. 2010;11(12):R123. doi: 10.1186/gb-2010-11-12-r123. Epub 2010 Dec 23.


Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis.

Obertello M, Krouk G, Katari MS, Runko SJ, Coruzzi GM.

BMC Syst Biol. 2010 Aug 12;4:111. doi: 10.1186/1752-0509-4-111.


Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution.

Cibrián-Jaramillo A, De la Torre-Bárcena JE, Lee EK, Katari MS, Little DP, Stevenson DW, Martienssen R, Coruzzi GM, DeSalle R.

Genome Biol Evol. 2010 Jul 12;2:225-39. doi: 10.1093/gbe/evq012.


Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana.

Vidal EA, Araus V, Lu C, Parry G, Green PJ, Coruzzi GM, Gutiérrez RA.

Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4477-82. doi: 10.1073/pnas.0909571107. Epub 2010 Feb 8.


Nitrate signaling: adaptation to fluctuating environments.

Krouk G, Crawford NM, Coruzzi GM, Tsay YF.

Curr Opin Plant Biol. 2010 Jun;13(3):266-73. doi: 10.1016/j.pbi.2009.12.003. Epub 2010 Jan 21. Review.


In silico evaluation of predicted regulatory interactions in Arabidopsis thaliana.

Nero D, Katari MS, Kelfer J, Tranchina D, Coruzzi GM.

BMC Bioinformatics. 2009 Dec 21;10:435. doi: 10.1186/1471-2105-10-435.


VirtualPlant: a software platform to support systems biology research.

Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutiérrez RA.

Plant Physiol. 2010 Feb;152(2):500-15. doi: 10.1104/pp.109.147025. Epub 2009 Dec 9.


A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling.

Ruffel S, Krouk G, Coruzzi GM.

Plant Physiol. 2010 Feb;152(2):445-52. doi: 10.1104/pp.109.148502. Epub 2009 Nov 25. No abstract available.


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. doi: 10.1371/journal.pone.0005764.


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. doi: 10.1186/1752-0509-3-59.


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. doi: 10.1007/s11103-009-9489-7. Epub 2009 May 2.


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. doi: 10.1371/journal.pcbi.1000326. Epub 2009 Mar 20.


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. doi: 10.1186/1752-0509-2-31.


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. doi: 10.1073/pnas.0800211105. Epub 2008 Mar 14.


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. doi: 10.1073/pnas.0709559105. Epub 2008 Jan 7.


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.


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.


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.


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.


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.


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.


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.


Systems biology for the virtual plant.

Gutiérrez RA, Shasha DE, Coruzzi GM.

Plant Physiol. 2005 Jun;138(2):550-4. Review. No abstract available.


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.


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.


Expressed sequence tag analysis in Cycas, the most primitive living seed plant.

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.

Genome Biol. 2003;4(12):R78. Epub 2003 Nov 18.


Achieving the in silico plant. Systems biology and the future of plant biological research.

Raikhel NV, Coruzzi GM.

Plant Physiol. 2003 Jun;132(2):404-9. No abstract available.

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