Jose Alonso Bellver

Yaschenko, A. E., Alonso, J. M., & Stepanova, A. N. (2024, February 27). Arabidopsis as a model for translational research. PLANT CELL, Vol. 2. https://doi.org/10.1093/plcell/koae065

Neubauer, M., Vollen, K., Ascencio-Ibanez, J. T., Hanley-Bowdoin, L., Stepanova, A. N., & Alonso, J. M. (2024, June 29). Development of modular geminivirus-based vectors for high cargo expression and gene targeting in plants. https://doi.org/10.1101/2024.06.29.601216

Vollen, K., Zhao, C., Alonso, J. M., & Stepanova, A. N. (2024). [Review of Sourcing DNA parts for synthetic biology applications in plants]. CURRENT OPINION IN BIOTECHNOLOGY, 87. https://doi.org/10.1016/j.copbio.2024.103140

Yaschenko, A. E., Fenech, M., Mazzoni-Putman, S., Alonso, J. M., & Stepanova, A. N. (2022). [Review of Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?]. CURRENT OPINION IN PLANT BIOLOGY, 68. https://doi.org/10.1016/j.pbi.2022.102241

Mallery, E. L., Yanagisawa, M., Zhang, C., Lee, Y., Robles, L. M., Alonso, J. M., & Szymanski, D. B. (2022). Tandem C2 domains mediate dynamic organelle targeting of a DOCK family guanine nucleotide exchange factor. JOURNAL OF CELL SCIENCE, 135(7). https://doi.org/10.1242/jcs.259825

Chen, H., Bullock, D. A., Jr., Alonso, J. M., & Stepanova, A. N. (2022). To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses. PLANTS-BASEL, 11(1). https://doi.org/10.3390/plants11010033

McFarlane, H. E., Mutwil-Anderwald, D., Verbancic, J., Picard, K. L., Gookin, T. E., Froehlich, A., … Persson, S. (2021). A G protein-coupled receptor-like module regulates cellulose synthase secretion from the endomembrane system in Arabidopsis. DEVELOPMENTAL CELL, 56(10), 1484-+. https://doi.org/10.1016/j.devcel.2021.03.031

Mazzoni-Putman, S. M., Brumos, J., Zhao, C., Alonso, J. M., & Stepanova, A. N. (2021). Auxin Interactions with Other Hormones in Plant Development. Cold Spring Harbor Perspectives in Biology, 13(10), a039990. https://doi.org/10.1101/cshperspect.a039990

Zhao, C., Yaschenko, A., Alonso, J. M., & Stepanova, A. N. (2021). [Review of Leveraging synthetic biology approaches in plant hormone research]. CURRENT OPINION IN PLANT BIOLOGY, 60. https://doi.org/10.1016/j.pbi.2020.10998

Brumos, J., Zhao, C., Gong, Y., Soriano, D., Patel, A. P., Perez-Amador, M. A., … Alonso, J. M. (2020). An Improved Recombineering Toolset for Plants. The Plant Cell. https://doi.org/10.1105/tpc.19.00431

Bagley, M. C., Stepanova, A. N., Ekelof, M., Alonso, J. M., & Muddiman, D. C. (2020). Development of a relative quantification method for infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings. RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 34(6). https://doi.org/10.1002/rcm.8616

Dolores Gomez, M., Barro-Trastoy, D., Fuster-Almunia, C., Tornero, P., Alonso, J. M., & Perez-Amador, M. A. (2020). Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY, 71(22), 7059–7072. https://doi.org/10.1093/jxb/eraa395

Barro‐Trastoy, D., Carrera, E., Baños, J., Palau‐Rodríguez, J., Ruiz‐Rivero, O., Tornero, P., … Pérez‐Amador, M. A. (2020). Regulation of ovule initiation by gibberellins and brassinosteroids in tomato and Arabidopsis: two plant species, two molecular mechanisms. The Plant Journal. https://doi.org/10.1111/tpj.14684

Perkins, P., Stepanova, A., Alonso, J., & Heber, S. (2020). RiboSimR: A Tool for Simulation and Power Analysis of Ribo-seq Data. In I. Măndoiu, T. Murali, G. Narasimhan, S. Rajasekaran, P. Skums, & A. Zelikovsky (Eds.), Computational Advances in Bio and Medical Sciences (pp. 121–133). https://doi.org/10.1007/978-3-030-46165-2_10

Brumos, J., Bobay, B. G., Clark, C. A., Alonso, J. M., & Stepanova, A. N. (2020). Structure–Function Analysis of Interallelic Complementation in ROOTY Transheterozygotes. Plant Physiology, 183(3), 1110–1125. https://doi.org/10.1104/pp.20.00310

Brumos, J., Zhao, C., Gong, Y., Soriano, D., Patel, A. P., Perez-Amador, M. A., … Alonso, J. M. (2019, June 3). An improved plant toolset for high-throughput recombineering (Vol. 6). Vol. 6. https://doi.org/10.1101/659276

Stepanova, A. N., & Alonso, J. M. (2019, July). From Ethylene-Auxin Interactions to Auxin Biosynthesis and Signal Integration. PLANT CELL, Vol. 31, pp. 1393–1394. https://doi.org/10.1105/tpc.19.00339

Dolores Gomez, M., Fuster-Almunia, C., Ocana-Cuesta, J., Alonso, J. M., & Perez-Amador, M. A. (2019). RGL2 controls flower development, ovule number and fertility in Arabidopsis. PLANT SCIENCE, 281, 82–92. https://doi.org/10.1016/j.plantsci.2019.01.014

Perkins, P., Mazzoni-Putman, S., Stepanova, A., Alonso, J., & Heber, S. (2019, June 6). RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data. BMC GENOMICS, Vol. 20. https://doi.org/10.1186/s12864-019-5700-7

Bhosale, R., Giri, J., Pandey, B. K., Giehl, R. F. H., Hartmann, A., Traini, R., … Swarup, R. (2018). A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate. Nature Communications, 9(1). https://doi.org/10.1038/S41467-018-03851-3

Bhosale, R., Giri, J., Pandey, B. K., Giehl, R. F. H., Hartmann, A., Traini, R., … Swarup, R. (2018). Author Correction: A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate. Nature Communications, 9(1), 1818. https://doi.org/10.1038/S41467-018-04281-X

Gomez, M. D., Barro-Trastoy, D., Escoms, E., Saura-Sánchez, M., Sánchez, I., Briones-Moreno, A., … Perez-Amador, M. A. (2018). Gibberellins negatively modulate ovule number in plants. Development, 145(13), dev163865. https://doi.org/10.1242/dev.163865

Brumos, J., Robles, L. M., Yun, J., Vu, T. C., Jackson, S., Alonso, J. M., & Stepanova, A. N. (2018). Local Auxin Biosynthesis Is a Key Regulator of Plant Development. DEVELOPMENTAL CELL, 47(3), 306-+. https://doi.org/10.1016/j.devcel.2018.09.022

Yanagisawa, M., Alonso, J. M., & Szymanski, D. B. (2018). Microtubule-Dependent Confinement of a Cell Signaling and Actin Polymerization Control Module Regulates Polarized Cell Growth. Current Biology, 28(15), 2459–2466.e4. https://doi.org/10.1016/J.CUB.2018.05.076

Estrada-Johnson, E., Csukasi, F., Pizarro, C. M., Vallarino, J. G., Kiryakova, Y., Vioque, A., … Valpuesta, V. (2017, July 24). Transcriptomic Analysis in Strawberry Fruits Reveals Active Auxin Biosynthesis and Signaling in the Ripe Receptacle (vol 8, pg 889, 2017). FRONTIERS IN PLANT SCIENCE, Vol. 8. https://doi.org/10.3389/fpls.2017.01305

Estrada-Johnson, E., Csukasi, F., Pizarro, C. M., Vallarino, J. G., Kiryakova, Y., Vioque, A., … Valpuesta, V. (2017). Transcriptomic analysis in strawberry fruits reveals active auxin biosynthesis and signaling in the ripe receptacle. Frontiers in Plant Science, 8.

Merchante, C., Stepanova, A. N., & Alonso, J. M. (2017). Translation regulation in plants: an interesting past, an exciting present and a promising future. PLANT JOURNAL, 90(4), 628–653. https://doi.org/10.1111/tpj.13520

Merchante, C., Yun, J., Valpuesta-Fernandez, V., Stepanova, A., & Alonso, J. (2017). Translation regulation of uORFs-containing genes in Arabidopsis.

Provart, N. J., Alonso, J., Assmann, S. M., Bergmann, D., Brady, S. M., Brkljacic, J., … Nemhauser, J. (2016). [Review of 50 years of Arabidopsis research: Highlights and future directions]. New Phytologist, 209(3), 921–944.

Merchante, C., Hu, Q., Heber, S., Alonso, J., & Stepanova, A. (2016). A Ribosome Footprinting Protocol for Plants. BIO-PROTOCOL, 6(21). https://doi.org/10.21769/bioprotoc.1985

Stepanova, A. N., & Alonso, J. M. (2016, September 27). Auxin catabolism unplugged: Role of IAA oxidation in auxin homeostasis. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol. 113, pp. 10742–10744. https://doi.org/10.1073/pnas.1613506113

Stepanova, A. N., & Alonso, J. M. (2016, December 5). Cutting Out the Middle Man in Light-Hormone Interactions. DEVELOPMENTAL CELL, Vol. 39, pp. 524–526. https://doi.org/10.1016/j.devcel.2016.11.013

Hu, Q. W., Merchante, C., Stepanova, A. N., Alonso, J. M., & Heber, S. (2016). Genome-wide search for translated upstream open reading frames in Arabidopsis thaliana. IEEE Transactions on Nanobioscience, 15(2), 150–159.

Merchante, C., Brumós, J., Yun, J., Stepanova, A., & Alonso, J. (2016). Hormone-Mediated Gene-Specific Translation Regulation. Retrieved from http://hdl.handle.net/10630/11885

Alonso, J. M., & Stepanova, A. N. (2015). A Recombineering-based gene tagging system for Arabidopsis. Bacterial Artificial Chromosomes, 2nd Edition, 1227, 233–243.

Hu, Q., Merchante, C., Stepanova, A. N., Alonso, J. M., & Heber, S. (2015). A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana. In Bioinformatics Research and Applications (Vol. 9096, pp. 138–149). https://doi.org/10.1007/978-3-319-19048-8_12

Hu, Q. W., Merchante, C., Stepanova, A. N., Alonso, J. M., & Heber, S. (2015). A stacking-based approach to identify translated upstream open reading frames in Arabidopsis thaliana. Bioinformatics research and applications (isbra 2015), 9096, 138–149.

Fabregas, N., Formosa-Jordan, P., Confraria, A., Siligato, R., Alonso, J. M., Swarup, R., … Ibanes, M. (2015). Auxin Influx Carriers Control Vascular Patterning and Xylem Differentiation in Arabidopsis thaliana. PLOS GENETICS, 11(4). https://doi.org/10.1371/journal.pgen.1005183

Moreno-Risueno, M. A., Sozzani, R., Yardimici, G. G., Petricka, J. J., Vernoux, T., Blilou, I., … Benfey, P. N. (2015). Bird and Scarecrow proteins organize tissue formation in Arabidopsis roots. Science, 350(6259), 426–430. https://doi.org/10.1126/science.aad1171

Worden, N., Wilkop, T. E., Esteve, V. E., Jeannotte, R., Lathe, R., Vernhettes, S., … Drakakaki, G. (2015). CESA TRAFFICKING INHIBITOR Inhibits Cellulose Deposition and Interferes with the Trafficking of Cellulose Synthase Complexes and Their Associated Proteins KORRIGAN1 and POM2/CELLULOSE SYNTHASE INTERACTIVE PROTEIN. Plant Physiology, 167(2), 381–393. https://doi.org/10.1104/pp.114.249003

Merchante, C., Brumos, J., Yun, J., Hu, Q., Spencer, K. R., Enriquez, P., … Alonso, J. M. (2015). Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2. CELL, 163(3), 684–697. https://doi.org/10.1016/j.cell.2015.09.036

Hu, Q. W., Merchante, C., Stepanova, A. N., Alonso, J., & Heber, S. (2015). Mining transcript features related to translation in Arabidopsis using LASSO and random forest. International conference on computational advances in bio and medical. https://doi.org/10.1109/iccabs.2015.7344713

Alonso, J. M., & Stepanova, A. N. (2015). Plant functional genomics methods and protocols second edition preface. Plant Functional Genomics: Methods and Protocols, 2nd Edition, 1284, V-.

Alonso, J., & STEPANOVA, A. N. N. A. (2015). Plant functional genomics: Methods and protocols. In J. M. Alonso & A. N. Stepanova (Eds.), Plant Functional Genomics: Methods and Protocols: Second Edition (2nd ed., pp. 1–526). https://doi.org/10.1007/978-1-4939-2444-8

Han, S. W., Alonso, J., & Rojas-Pierce, M. (2015). Regulator of bulb biogenesis1 (RBB1) is involved in vacuole bulb formation in arabidopsis. PLoS One, 10(4), e0125621. https://doi.org/10.1371/journal.pone.0125621

Alonso, J. M., & Stepanova, A. N. (2014). Arabidopsis Transformation with Large Bacterial Artificial Chromosomes. In Arabidopsis Protocols (pp. 271–283).

Brumos, J., Alonso, J. M., & Stepanova, A. N. (2014). Genetic aspects of auxin biosynthesis and its regulation. PHYSIOLOGIA PLANTARUM, 151(1), 3–12. https://doi.org/10.1111/ppl.12098

Band, L. R., Wells, D. M., Fozard, J. A., Ghetiu, T., French, A. P., Pound, M. P., … Hodgman, T. C. (2014). Systems analysis of auxin transport in the arabidopsis root apex. Plant Cell, 26(3), 862–875.

Catalá, R., López-Cobollo, R., Mar Castellano, M., Angosto, T., Alonso, J. M., Ecker, J. R., & Salinas, J. (2014). The Arabidopsis 14-3-3 Protein RARE COLD INDUCIBLE 1A Links Low-Temperature Response and Ethylene Biosynthesis to Regulate Freezing Tolerance and Cold Acclimation
 . The Plant Cell, 26(8), 3326–3342. https://doi.org/10.1105/tpc.114.127605

Pietra, S., Gustavsson, A., Kiefer, C., Kalmbach, L., Horstedt, P., Ikeda, Y., … Grebe, M. (2013). Arabidopsis SABRE and CLASP interact to stabilize cell division plane orientation and planar polarity. NATURE COMMUNICATIONS, 4. https://doi.org/10.1038/ncomms3779

Merchante, C., Alonso, J. M., & Stepanova, A. N. (2013). [Review of Ethylene signaling: simple ligand, complex regulation]. CURRENT OPINION IN PLANT BIOLOGY, 16(5), 554–560. https://doi.org/10.1016/j.pbi.2013.08.001

Hill, K., Mathews, D. E., Kim, H. J., Street, I. H., Wildes, S. L., Chiang, Y.-H., … Schaller, G. E. (2013). Functional Characterization of Type-B Response Regulators in the Arabidopsis Cytokinin Response
 
 . Plant Physiology, 162(1), 212–224. https://doi.org/10.1104/pp.112.208736

Kopycki, J., Wieduwild, E., Kohlschmidt, J., Brandt, W., Stepanova, A. N., Alonso, J. M., … Grubb, C. D. (2013). Kinetic analysis of Arabidopsis glucosyltransferase UGT74B1 illustrates a general mechanism by which enzymes can escape product inhibition. BIOCHEMICAL JOURNAL, 450(1), 37–46. https://doi.org/10.1042/bj20121403

Robert, H. S., Grones, P., Stepanova, A. N., Robles, L. M., Lokerse, A. S., Alonso, J. M., … Friml, J. (2013). Local Auxin Sources Orient the Apical-Basal Axis in Arabidopsis Embryos. CURRENT BIOLOGY, 23(24), 2506–2512. https://doi.org/10.1016/j.cub.2013.09.039

Robles, L., Stepanova, A., & Alonso, J. (2013). Molecular Mechanisms of EthyleneAuxin Interaction. MOLECULAR PLANT, 6(6), 1734–1737. https://doi.org/10.1093/mp/sst113

Robles, L., Stepanova, A., & Alonso, J. (2013). Molecular mechanisms of ethylene–auxin interactions. Molecular Plant, sst113.

Péret, B., Swarup, K., Ferguson, A., Seth, M., Yang, Y., Dhondt, S., … Syed, A. (2012). AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during Arabidopsis development. The Plant Cell Online, 24(7), 2874–2885. https://doi.org/10.1105/tpc.112.097766

Peret, B., Swarup, K., Ferguson, A., Seth, M., Yang, Y. D., Dhondt, S., … Laplaze, L. (2012). AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during arabidopsis development. Plant Cell, 24(7), 2874–2885.

He, W., Brumos, J., Li, H., Ji, Y., Ke, M., Gong, X., … Guo, H. (2011). A Small-Molecule Screen Identifies l-Kynurenine as a Competitive Inhibitor of TAA1/TAR Activity in Ethylene-Directed Auxin Biosynthesis and Root Growth in Arabidopsis. The Plant Cell, 23(11), 3944–3960. https://doi.org/10.1105/tpc.111.089029

Zhou, R., Benavente, L. M., Stepanova, A. N., & Alonso, J. M. (2011). A recombineering-based gene tagging system for Arabidopsis. PLANT JOURNAL, 66(4), 712–723. https://doi.org/10.1111/j.1365-313x.2011.04524.x

Stepanova, A. N., & Alonso, J. M. (2011, October 18). Bypassing Transcription: A Shortcut in Cytokinin-Auxin Interactions. DEVELOPMENTAL CELL, Vol. 21, pp. 608–610. https://doi.org/10.1016/j.devcel.2011.09.016

Stepanova, A. N., Yun, J., Robles, L. M., Novak, O., He, W., Guo, H., … Alonso, J. M. (2011). The Arabidopsis YUCCA1 Flavin Monooxygenase Functions in the Indole-3-Pyruvic Acid Branch of Auxin Biosynthesis. PLANT CELL, 23(11), 3961–3973. https://doi.org/10.1105/tpc.111.088047

Tsuchisaka, A., Yu, G., Jin, H., Alonso, J. M., Ecker, J. R., Zhang, X., … Theologis, A. (2009). A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana. Genetics, 183(3), 979–1003. https://doi.org/10.1534/genetics.109.107102

Stepanova, A. N., & Alonso, J. M. (2009). [Review of Ethylene signaling and response: where different regulatory modules meet]. CURRENT OPINION IN PLANT BIOLOGY, 12(5), 548–555. https://doi.org/10.1016/j.pbi.2009.07.009

Ikeda, Y., Men, S., Fischer, U., Stepanova, A. N., Alonso, J. M., Ljung, K., & Grebe, M. (2009). Local auxin biosynthesis modulates gradient-directed planar polarity in Arabidopsis. NATURE CELL BIOLOGY, 11(6), 731–U70. https://doi.org/10.1038/ncb1879

Hu, J., Mitchum, M. G., Barnaby, N., Ayele, B. T., Ogawa, M., Nam, E., … Ecker, J. R. (2008). Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis. The Plant Cell Online, 20(2), 320–336. https://doi.org/10.1105/tpc.107.057752

Stepanova, A. N., Robertson-Hoyt, J., Yun, J., Benavente, L. M., Xie, D.-Y., Doležal, K., … Alonso, J. M. (2008). TAA1-Mediated Auxin Biosynthesis Is Essential for Hormone Crosstalk and Plant Development. Cell, 133(1), 177–191. https://doi.org/10.1016/j.cell.2008.01.047

Leivar, P., Monte, E., Al-Sady, B., Carle, C., Storer, A., Alonso, J. M., … Quail, P. H. (2008). The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. The Plant Cell Online, 20(2), 337–352. https://doi.org/10.1105/tpc.107.052142

Li, H., He, Z., Lu, G., Lee, S. C., Alonso, J., Ecker, J. R., & Luan, S. (2007). A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis. PLANT CELL, 19(8), 2403–2416. https://doi.org/10.1105/tpc.107.053579

Ronan C. O'Malley, Alonso, J. M., Kim, C. J., Leisse, T. J., & Ecker, J. R. (2007). An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. NATURE PROTOCOLS, 2(11), 2910–2917. https://doi.org/10.1038/nprot.2007.425

Chekanova, J. A., Gregory, B. D., Reverdatto, S. V., Chen, H., Kumar, R., Hooker, T., … Peng, Q. (2007). Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the< i> Arabidopsis</i> Transcriptome. Cell, 131(7), 1340–1353. https://doi.org/10.1016/j.cell.2007.10.056

Stepanova, A. N., Yun, J., Likhacheva, A. V., & Alonso, J. M. (2007). Multilevel interactions between ethylene and auxin in Arabidopsis roots. PLANT CELL, 19(7), 2169–2185. https://doi.org/10.1105/tpc.107.052068

Mori, I. C., Murata, Y., Yang, Y., Munemasa, S., Wang, Y.-F., Andreoli, S., … Ecker, J. R. (2006). CDPKs CPK6 and CPK3 function in ABA regulation of guard cell S-type anion-and Ca2+-permeable channels and stomatal closure. PLoS Biology, 4(10), e327.

Rudella, A., Friso, G., Alonso, J. M., Ecker, J. R., & Wijk, K. J. (2006). Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis. PLANT CELL, 18(7), 1704–1721. https://doi.org/10.1105/tpc.106.042861

Kim, S. A., Punshon, T., Lanzirotti, A., Li, L., Alonso, J. M., Ecker, J. R., … Guerinot, M. L. (2006). Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1. SCIENCE, 314(5803), 1295–1298. https://doi.org/10.1126/science.1132563

Benavente, L. M., & Alonso, J. M. (2006). Molecular mechanisms of ethylene signaling in Arabidopsis. Molecular BioSystems, 2(3-4), 165. https://doi.org/10.1039/b513874d

Alonso, J., & Ecker, J. R. (2006). Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nature Reviews Genetics, 7(7), 524–536. https://doi.org/10.1038/nrg1893

Stepanova, A. N., & Alonso, J. M. (2006). PCR-based screening for insertional mutants. In Arabidopsis Protocols (pp. 163–172).

Lariguet, P., Schepens, I., Hodgson, D., Pedmale, U. V., Trevisan, M., Kami, C., … Liscum, E. (2006). PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism. Proceedings of the National Academy of Sciences, 103(26), 10134–10139. https://doi.org/10.1073/pnas.0603799103

Chen, J.-G., Ullah, H., Temple, B., Liang, J., Guo, J., Alonso, J. M., … Jones, A. M. (2006). RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis. Journal of Experimental Botany, 57(11), 2697–2708. https://doi.org/10.1093/jxb/erl035

Hutchison, C. E., Li, J., Argueso, C., Gonzalez, M., Lee, E., Lewis, M. W., … Alonso, J. M. (2006). The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling. The Plant Cell Online, 18(11), 3073–3087. https://doi.org/10.1105/tpc.106.045674

Pfund, C., Tans-Kersten, J., Dunning, F. M., Alonso, J. M., Ecker, J. R., Allen, C., & Bent, A. F. (2005). " Flagellin is not a major defense elicitor in Ralstonia solanacearum cells (vol 17, pg 696, 2005). MOLECULAR PLANT-MICROBE INTERACTIONS, 18(9), 1024.

Stepanova, A. N., Hoyt, J. M., Hamilton, A. A., & Alonso, J. M. (2005). A link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis. PLANT CELL, 17(8), 2230–2242. https://doi.org/10.1105/tpc.105.033365

Liu, G. S., Holub, E. B., Alonso, J. M., Ecker, JR, & Fobert, P. R. (2005). An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance. PLANT JOURNAL, 41(2), 304–318. https://doi.org/10.1111/j.1365-313x.2004.02296.x

Stepanova, A. N., & Alonso, J. M. (2005). Arabidopsis ethylene signaling pathway. Science Signaling, 2005(276), cm4.

Nagpal, P., Ellis, C. M., Weber, H., Ploense, S. E., Barkawi, L. S., Guilfoyle, T. J., … Farmer, E. E. (2005). Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development, 132(18), 4107–4118.

Prigge, M. J., Otsuga, D., Alonso, J. M., Ecker, J. R., Drews, G. N., & Clark, S. E. (2005). Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. The Plant Cell Online, 17(1), 61–76.

STEPANOVA, A. N. N. A., & Alonso, J. (2005). Ethylene signalling and response pathway: A unique signalling cascade with a multitude of inputs and outputs. Physiologia Plantarum, 123(2), 195–206. https://doi.org/10.1111/j/1399-3054.2004.00447

Okushima, Y., Overvoorde, P. J., Arima, K., Alonso, J. M., Chan, A., Chang, C., … Nguyen, D. (2005). Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. The Plant Cell Online, 17(2), 444–463.

Overvoorde, P. J., Okushima, Y., Alonso, J. M., Chan, A., Chang, C., Ecker, J. R., … Quach, H. (2005). Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana. The Plant Cell Online, 17(12), 3282–3300.

Mason, M. G., Mathews, D. E., Argyros, D. A., Maxwell, B. B., Kieber, J. J., Alonso, J. M., … Schaller, G. E. (2005). Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis. The Plant Cell Online, 17(11), 3007–3018.

Wilmoth, J. C., Wang, S., Tiwari, S. B., Joshi, A. D., Hagen, G., Guilfoyle, T. J., … Reed, J. W. (2005). NPH4/ARF7 and ARF19 promote leaf expansion and auxin‐induced lateral root formation. The Plant Journal, 43(1), 118–130.

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Novillo, F., Alonso, J. M., Ecker, J. R., & Salinas, J. (2004). CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. Proceedings of the National Academy of Sciences, 101(11), 3985–3990. https://doi.org/10.1073/PNAS.0303029101

Li, H., Johnson, P., Stepanova, A., Alonso, J. M., & Ecker, J. R. (2004). Convergence of signaling of differential cell growth pathways in the control in Arabidopsis. Developmental Cell, 7(2), 193–204. https://doi.org/10.1016/j.devcel.2004.07.002

Tyler, L., Thomas, S. G., Hu, J., Dill, A., Alonso, J. M., Ecker, J. R., & Sun, T.-ping. (2004). DELLA proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiology, 135(2), 1008–1019.

Pfund, C., Tans-Kersten, J., Dunning, F. M., Alonso, J. M., Ecker, JR, Allen, C., & Bent, A. F. (2004). Flagellin is not a major defense elicitor in Ralstonia solanacearum cells or extracts applied to Arabidopsis thaliana. MOLECULAR PLANT-MICROBE INTERACTIONS, 17(6), 696–706. https://doi.org/10.1094/MPMI.2004.17.6.696

Chen, J.-G., Pandey, S., Huang, J., Alonso, J. M., Ecker, J. R., Assmann, S. M., & Jones, A. M. (2004). GCR1 can act independently of heterotrimeric G-protein in response to brassinosteroids and gibberellins in Arabidopsis seed germination. Plant Physiology, 135(2), 907–915.

Mockler, T. C., Yu, X., Shalitin, D., Parikh, D., Michael, T. P., Liou, J., … Lin, C. (2004). Regulation of flowering time in Arabidopsis by K homology domain proteins. Proceedings of the National Academy of Sciences, 101(34), 12759–12764. https://doi.org/10.1073/PNAS.0404552101

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Monte, E., Tepperman, J. M., Al-Sady, B., Kaczorowski, K. A., Alonso, J. M., Ecker, J. R., … Quail, P. H. (2004). The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. Proceedings of the National Academy of Sciences, 101(46), 16091–16098. https://doi.org/10.1073/pnas.0407107101

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Mackey, D., Belkhadir, Y., Alonso, J. M., Ecker, J. R., & Dangl, J. L. (2003). < i> Arabidopsis</i> RIN4 Is a Target of the Type III Virulence Effector AvrRpt2 and Modulates RPS2-Mediated Resistance. Cell, 112(3), 379–389.

Lariguet, P., Boccalandro, H. E., Alonso, J. M., Ecker, J. R., Chory, J., Casal, J. J., & Fankhauser, C. (2003). A growth regulatory loop that provides homeostasis to phytochrome A signaling. The Plant Cell Online, 15(12), 2966–2978.

Strand, Å., Asami, T., Alonso, J., Ecker, J. R., & Chory, J. (2003). Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX. Nature, 421(6918), 79–83.

Michael, T. P., Salome, P. A., Hannah, J. Y., Spencer, T. R., Sharp, E. L., McPeek, M. A., … McClung, C. R. (2003). Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science, 302(5647), 1049–1053.

Alonso, J. M., Stepanova, A. N., Solano, R., Wisman, E., Ferrari, S., Ausubel, F. M., & Ecker, J. R. (2003). Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis. Proceedings of the National Academy of Sciences, 100(5), 2992–2997.

Larkin, R. M., Alonso, J. M., Ecker, J. R., & Chory, J. (2003). GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science, 299(5608), 902–906.

Alonso, J. M., Stepanova, A. N., Leisse, T. J., Kim, C. J., Chen, H., Shinn, P., … Cheuk, R. (2003). Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science, 301(5633), 653–657.

Alonso, J. M. (2003). Genome-wide insertional mutagenesis of Arabidopsis thaliana (vol 301, pg 653, 2003). Science, 301(5641), 1849.

Monte, E., Alonso, J. M., Ecker, J. R., Zhang, Y., Li, X., Young, J., … Quail, P. H. (2003). Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways. The Plant Cell Online, 15(9), 1962–1980.

Catalá, R., Santos, E., Alonso, J. M., Ecker, J. R., Martínez-Zapater, J. M., & Salinas, J. (2003). Mutations in the Ca2+/H+ transporter CAX1 increase CBF/DREB1 expression and the cold-acclimation response in Arabidopsis. The Plant Cell Online, 15(12), 2940–2951.

Alonso, J. M., & Stepanova, A. N. (2003). T-DNA mutagenesis in Arabidopsis. In Plant Functional Genomics (pp. 177–187). https://doi.org/10.1385/1-59259-413-1:177

Lariguet, P., Boccalandro, H. E., Alonso, J. M., Ecker, J. R., Chory, J., Casal, J. J., & Fankhausera, C. (2003). The Balance between phytochrome kinase substrate1 and PKS2 Provides Homeostasis for Phytochrome A Signaling in Arabidopsis. The Plant Cell Online.

Ullah, H., Chen, J.-G., Temple, B., Boyes, D. C., Alonso, J. M., Davis, K. R., … Jones, A. M. (2003). The β-subunit of the Arabidopsis G protein negatively regulates auxin-induced cell division and affects multiple developmental processes. The Plant Cell Online, 15(2), 393–409.

Hu, J., Aguirre, M., Peto, C., Alonso, J., Ecker, J., & Chory, J. (2002). A role for peroxisomes in photomorphogenesis and development of Arabidopsis. Science, 297(5580), 405–409.

Schroeder, D. F., Gahrtz, M., Maxwell, B. B., Cook, R. K., Kan, J. M., Alonso, J. M., … Chory, J. (2002). De-Etiolated 1 and Damaged DNA Binding Protein 1 Interact to Regulate< i> Arabidopsis</i> Photomorphogenesis. Current Biology, 12(17), 1462–1472.

Zheng, H., Bednarek, S. Y., Sanderfoot, A. A., Alonso, J., Ecker, J. R., & Raikhel, N. V. (2002). NPSN11 is a cell plate-associated SNARE protein that interacts with the syntaxin KNOLLE. Plant Physiology, 129(2), 530–539.

Friedrichsen, D. M., Nemhauser, J., Muramitsu, T., Maloof, J. N., Alonso, J., Ecker, J. R., … Chory, J. (2002). Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. Genetics, 162(3), 1445–1456.

Zhao, Y., Hull, A. K., Gupta, N. R., Goss, K. A., Alonso, J., Ecker, J. R., … Celenza, J. L. (2002). Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes & Development, 16(23), 3100–3112.

Jarillo, J. A., Capel, J., Tang, R.-H., Yang, H.-Q., Alonso, J. M., Ecker, J. R., & Cashmore, A. R. (2001). An Arabidopsis circadian clock component interacts with both CRY1 and phyB. Nature, 410(6827), 487–490.

Jarillo, J. A., Gabrys, H., Capel, J., Alonso, J. M., Ecker, J. R., & Cashmore, A. R. (2001). Phototropin-related NPL1 controls chloroplast relocation induced by blue light. Nature, 410(6831), 952–954.

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Hirayama, T., & Alonso, J. M. (2000). Ethylene captures a metal! Metal ions are involved in ethylene perception and signal transduction. Plant and Cell Physiology, 41(5), 548–555.

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