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Engineering Synthetic Signaling in Plants.

Leydon AR, Gala HP, Guiziou S, Nemhauser JL.

Annu Rev Plant Biol. 2020 Feb 24. doi: 10.1146/annurev-arplant-081519-035852. [Epub ahead of print]


Mapping and Dynamics of Regulatory DNA in Maturing Arabidopsis thaliana Siliques.

Sullivan AM, Arsovski AA, Thompson A, Sandstrom R, Thurman RE, Neph S, Johnson AK, Sullivan ST, Sabo PJ, Neri FV 3rd, Weaver M, Diegel M, Nemhauser JL, Stamatoyannopoulos JA, Bubb KL, Queitsch C.

Front Plant Sci. 2019 Nov 14;10:1434. doi: 10.3389/fpls.2019.01434. eCollection 2019.


Auxin promotion of seedling growth via ARF5 is dependent on the brassinosteroid-regulated transcription factors BES1 and BEH4.

Galstyan A, Nemhauser JL.

Plant Direct. 2019 Sep 4;3(9):e00166. doi: 10.1002/pld3.166. eCollection 2019 Sep.


Accelerating structure-function mapping using the ViVa webtool to mine natural variation.

Hamm MO, Moss BL, Leydon AR, Gala HP, Lanctot A, Ramos R, Klaeser H, Lemmex AC, Zahler ML, Nemhauser JL, Wright RC.

Plant Direct. 2019 Jul 26;3(7):e00147. doi: 10.1002/pld3.147. eCollection 2019 Jul.


Synthetic Bistability and Differentiation in Yeast.

Yang Y, Nemhauser JL, Klavins E.

ACS Synth Biol. 2019 May 17;8(5):929-936. doi: 10.1021/acssynbio.8b00524. Epub 2019 May 1.


The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family.

Galli M, Khakhar A, Lu Z, Chen Z, Sen S, Joshi T, Nemhauser JL, Schmitz RJ, Gallavotti A.

Nat Commun. 2018 Oct 30;9(1):4526. doi: 10.1038/s41467-018-06977-6.


Back to basics: what is the function of an Aux/IAA in auxin response?

Nemhauser JL.

New Phytol. 2018 Jun;218(4):1295-1297. doi: 10.1111/nph.15172. No abstract available.


Synthetic hormone-responsive transcription factors can monitor and re-program plant development.

Khakhar A, Leydon AR, Lemmex AC, Klavins E, Nemhauser JL.

Elife. 2018 May 1;7. pii: e34702. doi: 10.7554/eLife.34702.


Phytochrome B regulates resource allocation in Brassica rapa.

Arsovski AA, Zemke JE, Haagen BD, Kim SH, Nemhauser JL.

J Exp Bot. 2018 May 19;69(11):2837-2846. doi: 10.1093/jxb/ery080.


Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana.

Alexandre CM, Urton JR, Jean-Baptiste K, Huddleston J, Dorrity MW, Cuperus JT, Sullivan AM, Bemm F, Jolic D, Arsovski AA, Thompson A, Nemhauser JL, Fields S, Weigel D, Bubb KL, Queitsch C.

Mol Biol Evol. 2018 Apr 1;35(4):837-854. doi: 10.1093/molbev/msx326. Erratum in: Mol Biol Evol. 2018 Jul 1;35(7):1821.


Insights into the Evolution and Function of Auxin Signaling F-Box Proteins in Arabidopsis thaliana Through Synthetic Analysis of Natural Variants.

Wright RC, Zahler ML, Gerben SR, Nemhauser JL.

Genetics. 2017 Oct;207(2):583-591. doi: 10.1534/genetics.117.300092. Epub 2017 Jul 31.


Characterizing Auxin Response Circuits in Saccharomyces cerevisiae by Flow Cytometry.

Pierre-Jerome E, Wright RC, Nemhauser JL.

Methods Mol Biol. 2017;1497:271-281.


Functional analysis of molecular interactions in synthetic auxin response circuits.

Pierre-Jerome E, Moss BL, Lanctot A, Hageman A, Nemhauser JL.

Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11354-11359. Epub 2016 Sep 19.


Oligomerization of SCFTIR1 Is Essential for Aux/IAA Degradation and Auxin Signaling in Arabidopsis.

Dezfulian MH, Jalili E, Roberto DK, Moss BL, Khoo K, Nemhauser JL, Crosby WL.

PLoS Genet. 2016 Sep 12;12(9):e1006301. doi: 10.1371/journal.pgen.1006301. eCollection 2016 Sep.


A Live-imaging, Heat Shock-inducible System to Measure Aux/IAA Degradation Rates in Planta.

Guseman JM, Nemhauser JL, Moss BL.

Bio Protoc. 2016 Aug 5;6(15). pii: e1881. doi: 10.21769/BioProtoc.1881.


Plant synthetic biology for molecular engineering of signalling and development.

Nemhauser JL, Torii KU.

Nat Plants. 2016 Mar 2;2:16010. doi: 10.1038/nplants.2016.10. Review.


As above, so below: Auxin's role in lateral organ development.

Taylor-Teeples M, Lanctot A, Nemhauser JL.

Dev Biol. 2016 Nov 1;419(1):156-164. doi: 10.1016/j.ydbio.2016.03.020. Epub 2016 Mar 17. Review.


Auxin signaling modules regulate maize inflorescence architecture.

Galli M, Liu Q, Moss BL, Malcomber S, Li W, Gaines C, Federici S, Roshkovan J, Meeley R, Nemhauser JL, Gallavotti A.

Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13372-7. doi: 10.1073/pnas.1516473112. Epub 2015 Oct 13.


Untethering the TIR1 auxin receptor from the SCF complex increases its stability and inhibits auxin response.

Yu H, Zhang Y, Moss BL, Bargmann BO, Wang R, Prigge M, Nemhauser JL, Estelle M.

Nat Plants. 2015 Mar;1(3). pii: 14030.


Rate Motifs Tune Auxin/Indole-3-Acetic Acid Degradation Dynamics.

Moss BL, Mao H, Guseman JM, Hinds TR, Hellmuth A, Kovenock M, Noorassa A, Lanctot A, Villalobos LI, Zheng N, Nemhauser JL.

Plant Physiol. 2015 Sep;169(1):803-13. doi: 10.1104/pp.15.00587. Epub 2015 Jul 6.


New mechanistic links between sugar and hormone signalling networks.

Ljung K, Nemhauser JL, Perata P.

Curr Opin Plant Biol. 2015 Jun;25:130-7. doi: 10.1016/j.pbi.2015.05.022. Epub 2015 Jun 2. Review.


New tangles in the auxin signaling web.

Wright RC, Nemhauser JL.

F1000Prime Rep. 2015 Feb 3;7:19. doi: 10.12703/P7-19. eCollection 2015. Review.


Auxin-induced degradation dynamics set the pace for lateral root development.

Guseman JM, Hellmuth A, Lanctot A, Feldman TP, Moss BL, Klavins E, Calderón Villalobos LI, Nemhauser JL.

Development. 2015 Mar 1;142(5):905-9. doi: 10.1242/dev.117234. Epub 2015 Jan 29.


Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana.

Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, Thompson A, Neri FV 3rd, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes TR, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA.

Cell Rep. 2014 Sep 25;8(6):2015-2030. doi: 10.1016/j.celrep.2014.08.019. Epub 2014 Sep 15.


Recapitulation of the forward nuclear auxin response pathway in yeast.

Pierre-Jerome E, Jang SS, Havens KA, Nemhauser JL, Klavins E.

Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9407-12. doi: 10.1073/pnas.1324147111. Epub 2014 Jun 16.


The effects of DELLAs on growth change with developmental stage and brassinosteroid levels.

Stewart Lilley JL, Gan Y, Graham IA, Nemhauser JL.

Plant J. 2013 Oct;76(1):165-73. doi: 10.1111/tpj.12280. Epub 2013 Aug 5.


Tuning the auxin transcriptional response.

Pierre-Jerome E, Moss BL, Nemhauser JL.

J Exp Bot. 2013 Jun;64(9):2557-63. doi: 10.1093/jxb/ert100. Epub 2013 Apr 29. Review.


Mutations in the TIR1 auxin receptor that increase affinity for auxin/indole-3-acetic acid proteins result in auxin hypersensitivity.

Yu H, Moss BL, Jang SS, Prigge M, Klavins E, Nemhauser JL, Estelle M.

Plant Physiol. 2013 May;162(1):295-303. doi: 10.1104/pp.113.215582. Epub 2013 Mar 28.


Auxin 2012: a rich mea ho'oulu.

Strader LC, Nemhauser JL.

Development. 2013 Mar;140(6):1153-7. doi: 10.1242/dev.090530.


The protein chaperone HSP90 can facilitate the divergence of gene duplicates.

Lachowiec J, Lemus T, Thomas JH, Murphy PJ, Nemhauser JL, Queitsch C.

Genetics. 2013 Apr;193(4):1269-77. doi: 10.1534/genetics.112.148098. Epub 2013 Feb 14.


An endogenous carbon-sensing pathway triggers increased auxin flux and hypocotyl elongation.

Lilley JL, Gee CW, Sairanen I, Ljung K, Nemhauser JL.

Plant Physiol. 2012 Dec;160(4):2261-70. doi: 10.1104/pp.112.205575. Epub 2012 Oct 16.


A synthetic approach reveals extensive tunability of auxin signaling.

Havens KA, Guseman JM, Jang SS, Pierre-Jerome E, Bolten N, Klavins E, Nemhauser JL.

Plant Physiol. 2012 Sep;160(1):135-42. doi: 10.1104/pp.112.202184. Epub 2012 Jul 27.



Arsovski AA, Galstyan A, Guseman JM, Nemhauser JL.

Arabidopsis Book. 2012;10:e0147. doi: 10.1199/tab.0147. Epub 2012 Jan 31.


Bipartite promoter element required for auxin response.

Walcher CL, Nemhauser JL.

Plant Physiol. 2012 Jan;158(1):273-82. doi: 10.1104/pp.111.187559. Epub 2011 Nov 18.


PIF genes mediate the effect of sucrose on seedling growth dynamics.

Stewart JL, Maloof JN, Nemhauser JL.

PLoS One. 2011;6(5):e19894. doi: 10.1371/journal.pone.0019894. Epub 2011 May 23.


Do trees grow on money? Auxin as the currency of the cellular economy.

Stewart JL, Nemhauser JL.

Cold Spring Harb Perspect Biol. 2010 Feb;2(2):a001420. doi: 10.1101/cshperspect.a001420. Review.


Cell signalling and gene regulation.

Lohmann JU, Nemhauser JL.

Curr Opin Plant Biol. 2009 Oct;12(5):517-9. doi: 10.1016/j.pbi.2009.09.001. Epub 2009 Sep 23. No abstract available.


Steroids are required for epidermal cell fate establishment in Arabidopsis roots.

Kuppusamy KT, Chen AY, Nemhauser JL.

Proc Natl Acad Sci U S A. 2009 May 12;106(19):8073-6. doi: 10.1073/pnas.0811633106. Epub 2009 Apr 28.


Cross-regulatory mechanisms in hormone signaling.

Kuppusamy KT, Walcher CL, Nemhauser JL.

Plant Mol Biol. 2009 Mar;69(4):375-81. doi: 10.1007/s11103-008-9389-2. Epub 2008 Aug 26. Review.


Integration of auxin and brassinosteroid pathways by Auxin Response Factor 2.

Vert G, Walcher CL, Chory J, Nemhauser JL.

Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9829-34. doi: 10.1073/pnas.0803996105. Epub 2008 Jul 3.


Dawning of a new era: photomorphogenesis as an integrated molecular network.

Nemhauser JL.

Curr Opin Plant Biol. 2008 Feb;11(1):4-8. Epub 2007 Nov 28. Review.


RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.

Hong F, Breitling R, McEntee CW, Wittner BS, Nemhauser JL, Chory J.

Bioinformatics. 2006 Nov 15;22(22):2825-7. Epub 2006 Sep 18.


Molecular mechanisms of steroid hormone signaling in plants.

Vert G, Nemhauser JL, Geldner N, Hong F, Chory J.

Annu Rev Cell Dev Biol. 2005;21:177-201. Review.


A new FronTIR in targeted protein degradation and plant development.

Nemhauser JL, Chory J.

Cell. 2005 Jul 1;121(7):970-2. Review.


Interdependency of brassinosteroid and auxin signaling in Arabidopsis.

Nemhauser JL, Mockler TC, Chory J.

PLoS Biol. 2004 Sep;2(9):E258. Epub 2004 Aug 24.


BRing it on: new insights into the mechanism of brassinosteroid action.

Nemhauser JL, Chory J.

J Exp Bot. 2004 Jan;55(395):265-70. Epub 2003 Dec 12. Review.


Building integrated models of plant growth and development.

Nemhauser JL, Maloof JN, Chory J.

Plant Physiol. 2003 Jun;132(2):436-9. No abstract available.


Auxin and ETTIN in Arabidopsis gynoecium morphogenesis.

Nemhauser JL, Feldman LJ, Zambryski PC.

Development. 2000 Sep;127(18):3877-88.


Auxin signaling in Arabidopsis flower development?

Nemhauser JL, Zambryski PC, Roe JL.

Curr Opin Plant Biol. 1998 Dec;1(6):531-5. Review. No abstract available.


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