Zahir Ali, Aala Abulfaraj, Ali Idris, Shakila Ali, Manal Tashkandi and Magdy M. Mahfouz. CRISPR/Cas9-mediated viral interference in plants. Genome Biology 2015, 16:238  doi:10.1186/s13059-015-0799-6

Bigeard J, Colcombet J, Hirt H., Signaling Mechanisms in Pattern-Triggered Immunity (PTI).​ Molecular Plant. 2015 Jan 9. pii: S1674-2052(15)00087-8. doi: 10.1016/j.molp.2014.12.022. PMID 25744358​

Yousef S. Al-Hafedh, Aftab Alam and Alejandro H. Buschmann, Bioremediation potential, growth and biomass yield of the green seaweed, Ulva lactuca in an integrated marine aquaculture system at the Red Sea coast of Saudi Arabia at different stocking densities and effluent flow rates. Aquaculture 2014, DOI: 10.1111/raq.12060.

Jégu T, Latrasse D, Delarue M, Hirt H, Domenichini S, Ariel F, Crespi M, Bergounioux C, Raynaud C, Benhamed M​., The BAF60 Subunit of the SWI/SNF Chromatin-Remodeling Complex Directly Controls the Formation of a Gene Loop at FLOWERING LOCUS C in Arabidopsis.​ Plant Cell. 2014 Feb;26(2):538-51. doi: 10.1105/tpc.113.114454. PMID: 24510722​

Ovečka M, Takáč T, Komis G, Vadovič P, Bekešová S, Doskočilová A, Smékalová V, Luptovčiak I, Samajová O, Schweighofer A, Meskiene I, Jonak C, Křenek P, Lichtscheidl I, Skultéty L, Hirt H​, Samaj J., Salt-induced subcellular kinase relocation and seedling susceptibility caused by overexpression of Medicago SIMKK in Arabidopsis, Molecular Cell.  2014 Jun;65(9):2335-50. doi: 10.1093/jxb/eru115. Epub 2014 Mar 19. PMID: 24648569​​

Hudik E, Berriri S, Hirt H​, Colcombet J., Identification of Constitutively Active AtMPK6 Mutants Using a Functional Screen in Saccharomyces cerevisiae. Methods Molecular Biology. 2014;1171:67-77. doi: 10.1007/978-1-4939-0922-3_6. PMID: 24908120​​​

Bigeard J, Pflieger D, Colcombet J, Gérard L, Mireau H, Hirt H​.​, Protein Complexes Characterization in Arabidopsis thaliana by Tandem Affi nity Purifi cation Coupled to Mass Spectrometry Analysis. Methods Molecular Biology. 2014;1171:237-50. doi: 10.1007/978-1-4939-0922-3_18. PMID: 24908132

Neumann C, Fraiture M, Hernàndez-Reyes C, Akum FN, Virlogeux-Payant I, Chen Y, Pateyron S, Colcombet J, Kogel KH, Hirt H​, Brunner F, Schikora A., The Salmonella effector protein SpvC, a phosphothreonine lyase is functional in plant cells. Frontiers In Microbiology. 2014 Oct 17;5:548. doi: 10.3389/fmicb.2014.00548. eCollection 2014.​​

Zourelidou M, Absmanner B, Weller B, Barbosa IC, Willige BC, Fastner A, Streit V, Port SA, Colcombet J, de la Fuente van Bentem S, Hirt H​, Kuster B, Schulze WX, Hammes UZ, Schwechheimer C., Auxin efflux by PIN-FORMED proteins is activated by two different protein kinases, D6 PROTEIN KINASE and PINOID.​ Elife. 2014 Jun 19:e02860. doi: 10.7554/eLife.02860. PMID: 24948515

Bigeard J, Rayapuram N​, Pflieger D, Hirt H.​​ Phosphorylation-dependent regulation of plant chromatin and chromatinassociated proteins. Proteomics. 2014 May 31. doi: 10.1002/pmic.201400073. PMID: 24889195​

Bigeard J, Rayapuram N, Bonhomme L, Hirt H​, Pflieger D.​, Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana.​ Proteomics. 2014 May 31. doi: 10.1002/pmic.201400072 PMID: 24889360

Frei Dit Frey N, Garcia AV, Bigeard J, Zaag R, Bueso E, Garmier M, Pateyron S, de Tauzia-Moreau ML, Brunaud V, Balzergue S, Colcombet J, Aubourg S, Martin-Magniette ML, Hirt H​., Functional analysis of Arabidopsis immune-related MAPKs uncovers a role for MPK3 as negative regulator of inducible defences. Genome Biology. 2014 Jun 30;15(6):R87. PMID: 24980080​​

Honsdorf N, March TJ, Berger B, Tester M​, Pillen K. High-Throughput, Phenotyping to Detect Drought Tolerance QTL in Wild Barley Introgression Lines. PLoS One. 2014 May 13;9(5):e97047. doi: 10.1371/journal.pone.0097047. eCollection 2014. PubMed PMID: 24823485.

M. Aouida​, K. Kim, A.R. Shaikh, J.M. Pardo, J. Eppinger, D.-J. Yun, R.A. Bressan and M.L. Narasimhan. A Saccharomyces cerevisiae Assay System to Investigate Ligand/AdipoR1 Interactions That Lead to Cellular Signaling. Plos One, 8, (2013). 10.1371/journal.pone.0065454.

Garcia AV, Charrier A, Schikora A, Bigeard J, Pateyron S, de Tauzia-Moreau ML, Evrard A, Mithöfer A, Martin-Magniette ML, Virlogeux-Payant I, Hirt H​., Salmonella enterica flagellin is recognized via FLS2 and activates PAMP-triggered immunity in Arabidopsis thaliana.​ Molecular Plant. 2013 Nov 6. PMID: 24198231​

Li, L., A. Atef, A. Piatek, Z. Ali, M. Piatek, M. Aouida​, A. Sharakuu, A. Mahjoub, G. Wang, S. Khan, N. V. Fedoroff, J. K. Zhu and M. M. Mahfouz (2013). "Characterization and DNA-Binding Specificities of Ralstonia TAL-Like Effectors." Molecular Plant. (4):1318-30.​

Garnett, T., Conn, V., Plett, D., Conn, S., Zanghellini, J., Mackenzie, N., Enju, A., Francis, K., Holtham, L., Roessner, U., Boughton, B., Bacic, A., Shirley, N., Rafalski, A., Dhugga, K., Tester, M​ & Kaiser, B. (2013) The response of the maize nitrate transport system to nitrogen demand and supply across the lifecycle. New Phytologist 198: 82-94

Díaz-Sánchez V, Estrada AF, Limón MC, Al-Babili S​, Avalos J. The oxygenase CAO-1 of Neurospora crassa is a resveratrol cleavage enzyme. Eukaryot Cell. 2013  Sep;12(9):1305-14. doi: 10.1128/EC.00084-13. Epub 2013 Jul 26. PubMed PMID: 23893079.

B. Khraiwesh, J.-K. Zhu and J. Zhu. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms, 1819, 137-148, (2012). 10.1016/j.bbagrm.2011.05.001

M. Dassanayake, D.-H. Oh, J.S. Haas, A. Hernandez, H. Hong, S. Ali, D.-J. Yun, R.A. Bressan, J.-K. Zhu, H.J. Bohnert and J.M. Cheeseman. The genome of the extremophile crucifer Thellungiella parvula. Nature Genetics, 43, 913-U137, (2011). 10.1038/ng.889

H. Fujii, P.E. Verslues, J.-K. Zhu. Arabidopsis decuple mutant reveals the importance of SnRK2 kinases in osmotic stress responses in viv​o. Proceedings of the National Academy of Sciences of the United States of America, 108, 1717-1722, (2011). 10.1073/pnas.1018367108​​

Z. Gong and J.-K. Zhu. Cell Research, 21, 1649-1651, (2011). 10.1038/cr.2011.140

X.-J. He, T. Chen and J.-K. Zhu. Regulation and function of DNA methylation in plants and animals. Cell Research, 21, 442-465, (2011). 10.1038/cr.2011.23

C. Jiang, A. Mithani, X. Gan, E.J. Belfield, J.P. Klingler, J.-K. Zhu, J. Ragoussis, R. Mott and N.P. Harberd. Regenerant Arabidopsis Lineages Display a Distinct Genome-Wide Spectrum of Mutations Conferring Variant Phenotypes​. Current Biology, 21, 1385-1390, (2011). 10.1016/j.cub.2011.07.002

H. La, B. Ding, G.P. Mishra, B. Zhou, H. Yang, M.d.R. Bellizzi, S. Chen, B.C. Meyers, Z. Peng, J.-K. Zhu and G.-L. Wang. A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice. Proceedings of the National Academy of Sciences of the United States of America, 108, 15498-15503, (2011). 10.1073/pnas.1112704108

F.J. Quintero, J. Martinez-Atienza, I. Villalta, X. Jiang, W.-Y. Kim, Z. Ali, H. Fujii, I. Mendoza, D.-J. Yun, J.-K. Zhu and J.M. Pardo. Activation of the plasma membrane Na/H antiporter Salt-Overly-Sensitive 1 (SOS1) by phosphorylation of an auto-inhibitory C-terminal domain. Proceedings of the National Academy of Sciences of the United States of America, 108, 2611-2616, (2011). 10.1073/pnas.1018921108​

C. Yunta, M. Martinez-Ripoll, J.-K. Zhu and A. Allbert. The Structure of Arabidopsis thaliana OST1 Provides Insights into the Kinase Regulation Mechanism in Response to Osmotic Stress. Journal of Molecular Biology, 414, 135-144, (2011). 10.1016/j.jmb.2011.09.041

H. Chen, B. Zhang, L.M. Hicks and L. Xiong. A Nucleotide Metabolite Controls Stress-Responsive Gene Expression and Plant Development. Plos One, 6, (2011). 10.1371/journal.pone.0026661

B. Li, Q. Li, Y. Su, H. Chen, L. Xiong, G. Mi, H.J. Kronzucker and W. Shi. Shoot-supplied ammonium targets the root auxin influx carrier AUX1 and inhibits lateral root emergence in Arabidopsis. Plant Cell and Environment, 34, 933-946, (2011). 10.1111/j.1365-3040.2011.02295.x

Z. Gao, H.-L. Liu, L. Daxinger, O. Pontes, X. He, W. Qian, H. Lin, M. Xie, Z.J. Lorkovic, S. Zhang, D. Miki, X. Zhan, D. Pontier, T. Lagrange, H. Jin, A.J.M. Matzke, M. Matzke, C.S. Pikaard and J.-K. Zhu. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature, 465, 106-U118, (2010). 10.1038/nature09025

H. Jin and J.-K. Zhu. How Many Ways Are There to Generate Small RNAs​. Molecular Cell, 38, 775-777, (2010). 10.1016/j.molcel.2010.06.004​

H. Jin and J.-K. Zhu. A viral suppressor protein inhibits host RNA silencing by hooking up with Argonautes. Genes & Development, 24, 853-856, (2010). 10.1101/gad.1927310

J.P. Klingler, G. Batelli and J.-K. Zhu. ABA receptors: the START of a new paradigm in phytohormone signalling. Journal of Experimental Botany, 61, 3199-3210, (2010). 10.1093/jxb/erq151​

J.A. Law, I. Ausin, L.M. Johnson, A.A. Vashisht, J.-K. Zhu, J.A. Wohlschlegel and S.E. Jacobsen. A Protein Complex Required for Polymerase V Transcripts and RNA-Directed DNA Methylation in Arabidopsis. Current Biology, 20, 951-956, (2010). 10.1016/j.cub.2010.03.062

K. Melcher, Y. Xu, L.-M. Ng, X.E. Zhou, F.-F. Soon, V. Chinnusamy, K.M. Suino-Powell, A. Kovach, F.S. Tham, S.R. Cutler, J. Li, E.-L. Yong, J.-K. Zhu and H.E. Xu. Identification and mechanism of ABA receptor antagonism. Nature Structural & Molecular Biology, 17, 1102-U1110, (2010). 10.1038/nsmb.1887​

Z. Ren, Z. Zheng, V. Chinnusamy, J. Zhu, X. Cui, K. Iida and J.-K. Zhu. RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 107, 5669-5674, (2010). 10.1073/pnas.0910798107

Z. Zheng, Y. Xing, X.-J. He, W. Li, Y. Hu, S.K. Yadav, J. Oh and J.-K. Zhu. An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis. Plant Journal, 62, 92-99, (2010). 10.1111/j.1365-313X.2010.04130.x

J. Zhu, B.-H. Lee, M. Dellinger, X. Cui, C. Zhang, S. Wu, E.A. Nothnagel and J.-K. Zhu. Plant Journal, 63, 128-140, (2010). 10.1111/j.1365-313X.2010.04227.x

H. Chen, K. Saksa, F. Zhao, J. Qiu and L. Xiong. Genetic analysis of pathway regulation for enhancing branched-chain amino acid biosynthesis in plants. Plant Journal, 63, 573-583, (2010). 10.1111/j.1365-313X.2010.04261.x​

H. Chen and L. Xiong. The bifunctional abiotic stress signalling regulator and endogenous RNA silencing suppressor FIERY1 is required for lateral root formation. Plant Cell and Environment, 33, 2180-2190, (2010). 10.1111/j.1365-3040.2010.02218.x

H. Chen and L. Xiong. Myo-Inositol-1-phosphate Synthase Is Required for Polar Auxin Transport and Organ Development. Journal of Biological Chemistry, 285, 24238-24247, (2010). 10.1074/jbc.M110.123661

H. Fujii, V. Chinnusamy, A. Rodrigues, S. Rubio, R. Antoni, S.-Y. Park, S.R. Cutler, J. Sheen, P.L. Rodriguez and J.-K. Zhu. In vitro reconstitution of an abscisic acid signalling pathway. Nature, 462, 660-U138, (2009). 10.1038/nature08599

K. Melcher, L.-M. Ng, X.E. Zhou, F.-F. Soon, Y. Xu, K.M. Suino-Powell, S.-Y. Park, J.J. Weiner, H. Fujii, V. Chinnusamy, A. Kovach, J. Li, Y. Wang, J. Li, F.C. Peterson, D.R. Jensen, E.-L. Yong, B.F. Volkman, S.R. Cutler, J.-K. Zhu and H.E. Xu. A gate-latch-lock mechanism for hormone signalling by abscisic acid receptors. Nature, 462, 602-U672, (2009). 10.1038/nature08613