@misc{yaschenko_fenech_mazzoni-putman_alonso_stepanova_2022, title={Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?}, DOI={10.1016/j.pbi.2022.102241}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Yaschenko, Anna E. and Fenech, Mario and Mazzoni-Putman, Serina and Alonso, Jose M. and Stepanova, Anna N.}, year={2022}, month={Aug} }
 @article{mallery_yanagisawa_zhang_lee_robles_alonso_szymanski_2022, title={Tandem C2 domains mediate dynamic organelle targeting of a DOCK family guanine nucleotide exchange factor}, volume={135}, DOI={10.1242/jcs.259825}, number={7}, journal={JOURNAL OF CELL SCIENCE}, publisher={The Company of Biologists}, author={Mallery, Eileen L. and Yanagisawa, Makoto and Zhang, Chunhua and Lee, Youngwoo and Robles, Linda M. and Alonso, Jose M. and Szymanski, Daniel B.}, year={2022}, month={Apr} }
 @article{chen_bullock_alonso_stepanova_2022, title={To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses}, volume={1}, DOI={10.3390/plants11010033}, journal={PLANTS-BASEL}, author={Chen, Hao and Bullock, David A., Jr. and Alonso, Jose M. and Stepanova, Anna N.}, year={2022}, month={Jan} }
 @article{mcfarlane_mutwil-anderwald_verbancic_picard_gookin_froehlich_chakravorty_trindade_alonso_assmann_et al._2021, title={A G protein-coupled receptor-like module regulates cellulose synthase secretion from the endomembrane system in Arabidopsis}, volume={5}, DOI={10.1016/j.devcel.2021.03.031}, journal={DEVELOPMENTAL CELL}, author={McFarlane, Heather E. and Mutwil-Anderwald, Daniela and Verbancic, Jana and Picard, Kelsey L. and Gookin, Timothy E. and Froehlich, Anja and Chakravorty, David and Trindade, Luisa M. and Alonso, Jose M. and Assmann, Sarah M. and et al.}, year={2021}, month={May} }
 @article{mazzoni-putman_brumos_zhao_alonso_stepanova_2021, title={Auxin Interactions with Other Hormones in Plant Development}, volume={13}, ISSN={1943-0264}, url={http://dx.doi.org/10.1101/cshperspect.a039990}, DOI={10.1101/cshperspect.a039990}, number={10}, journal={Cold Spring Harbor Perspectives in Biology}, publisher={Cold Spring Harbor Laboratory}, author={Mazzoni-Putman, Serina M. and Brumos, Javier and Zhao, Chengsong and Alonso, Jose M. and Stepanova, Anna N.}, year={2021}, month={Apr}, pages={a039990} }
 @misc{zhao_yaschenko_alonso_stepanova_2021, title={Leveraging synthetic biology approaches in plant hormone research}, DOI={10.1016/j.pbi.2020.10998}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Zhao, Chengsong and Yaschenko, Anna and Alonso, Jose M. and Stepanova, Anna N.}, year={2021}, month={Apr} }
 @article{brumos_zhao_gong_soriano_patel_perez-amador_stepanova_alonso_2020, title={An Improved Recombineering Toolset for Plants}, volume={32}, DOI={10.1105/tpc.19.00431}, number={1}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Brumos, Javier and Zhao, Chengsong and Gong, Yan and Soriano, David and Patel, Arjun P. and Perez-Amador, Miguel A. and Stepanova, Anna N. and Alonso, Jose M.}, year={2020}, month={Jan}, pages={100–122} }
 @article{bagley_stepanova_ekelof_alonso_muddiman_2020, title={Development of a relative quantification method for infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings}, volume={34}, ISBN={1097-0231}, DOI={10.1002/rcm.8616}, number={6}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Bagley, M. Caleb and Stepanova, Anna N. and Ekelof, Mans and Alonso, Jose M. and Muddiman, David C.}, year={2020} }
 @article{dolores gomez_barro-trastoy_fuster-almunia_tornero_alonso_perez-amador_2020, title={Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis}, volume={71}, ISBN={1460-2431}, DOI={10.1093/jxb/eraa395}, number={22}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Dolores Gomez, Maria and Barro-Trastoy, Daniela and Fuster-Almunia, Clara and Tornero, Pablo and Alonso, Jose M. and Perez-Amador, Miguel A.}, year={2020}, pages={7059–7072} }
 @article{barro‐trastoy_carrera_baños_palau‐rodríguez_ruiz‐rivero_tornero_alonso_lópez‐díaz_gómez_pérez‐amador_2020, title={Regulation of ovule initiation by gibberellins and brassinosteroids in tomato and Arabidopsis: two plant species, two molecular mechanisms}, volume={102}, DOI={10.1111/tpj.14684}, number={5}, journal={The Plant Journal}, publisher={Wiley}, author={Barro‐Trastoy, Daniela and Carrera, Esther and Baños, Jorge and Palau‐Rodríguez, Julia and Ruiz‐Rivero, Omar and Tornero, Pablo and Alonso, José M. and López‐Díaz, Isabel and Gómez, María Dolores and Pérez‐Amador, Miguel A.}, year={2020}, month={Jun}, pages={1026–1041} }
 @inbook{perkins_stepanova_alonso_heber_2020, place={Cham, Switzerland}, series={Lecture Notes in Computer Science}, title={RiboSimR: A Tool for Simulation and Power Analysis of Ribo-seq Data}, ISBN={9783030461645 9783030461652}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/978-3-030-46165-2_10}, DOI={10.1007/978-3-030-46165-2_10}, booktitle={Computational Advances in Bio and Medical Sciences}, publisher={Springer International Publishing}, author={Perkins, Patrick and Stepanova, Anna and Alonso, Jose and Heber, Steffen}, editor={Măndoiu, I. and Murali, T. and Narasimhan, G. and Rajasekaran, S. and Skums, P. and Zelikovsky, A.Editors}, year={2020}, pages={121–133}, collection={Lecture Notes in Computer Science} }
 @article{brumos_bobay_clark_alonso_stepanova_2020, title={Structure–Function Analysis of Interallelic Complementation in ROOTY Transheterozygotes}, volume={183}, DOI={10.1104/pp.20.00310}, number={3}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={Brumos, Javier and Bobay, Benjamin G. and Clark, Cierra A. and Alonso, Jose M. and Stepanova, Anna N.}, year={2020}, month={Jul}, pages={1110–1125} }
 @article{brumos_zhao_gong_soriano_patel_perez-amador_stepanova_alonso_2019, title={An improved plant toolset for high-throughput recombineering}, volume={6}, DOI={10.1101/659276}, publisher={Cold Spring Harbor Laboratory}, author={Brumos, J. and Zhao, C. and Gong, Y. and Soriano, D. and Patel, A.P. and Perez-Amador, M.A. and Stepanova, A.N. and Alonso, J.M}, year={2019}, month={Jun} }
 @article{stepanova_alonso_2019, title={From Ethylene-Auxin Interactions to Auxin Biosynthesis and Signal Integration}, volume={31}, ISBN={1532-298X}, DOI={10.1105/tpc.19.00339}, number={7}, journal={PLANT CELL}, publisher={American Society of Plant Biologists (ASPB)}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2019}, month={Jul}, pages={1393–1394} }
 @article{dolores gomez_fuster-almunia_ocana-cuesta_alonso_perez-amador_2019, title={RGL2 controls flower development, ovule number and fertility in Arabidopsis}, volume={281}, ISBN={0168-9452}, DOI={10.1016/j.plantsci.2019.01.014}, journal={PLANT SCIENCE}, author={Dolores Gomez, Maria and Fuster-Almunia, Clara and Ocana-Cuesta, Javier and Alonso, Jose M. and Perez-Amador, Miguel A.}, year={2019}, month={Apr}, pages={82–92} }
 @article{perkins_mazzoni-putman_stepanova_alonso_heber_2019, title={RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data}, volume={20}, ISBN={1471-2164}, DOI={10.1186/s12864-019-5700-7}, journal={BMC GENOMICS}, author={Perkins, Patrick and Mazzoni-Putman, Serina and Stepanova, Anna and Alonso, Jose and Heber, Steffen}, year={2019} }
 @article{bhosale_giri_pandey_giehl_hartmann_traini_truskina_leftley_hanlon_swarup_et al._2018, title={A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/S41467-018-03851-3}, DOI={10.1038/S41467-018-03851-3}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Bhosale, Rahul and Giri, Jitender and Pandey, Bipin K. and Giehl, Ricardo F. H. and Hartmann, Anja and Traini, Richard and Truskina, Jekaterina and Leftley, Nicola and Hanlon, Meredith and Swarup, Kamal and et al.}, year={2018}, month={Apr} }
 @article{bhosale_giri_pandey_giehl_hartmann_traini_truskina_leftley_hanlon_swarup_et al._2018, title={Author Correction: A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/S41467-018-04281-X}, DOI={10.1038/S41467-018-04281-X}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Bhosale, Rahul and Giri, Jitender and Pandey, Bipin K. and Giehl, Ricardo F. H. and Hartmann, Anja and Traini, Richard and Truskina, Jekaterina and Leftley, Nicola and Hanlon, Meredith and Swarup, Kamal and et al.}, year={2018}, month={May} }
 @article{gomez_barro-trastoy_escoms_saura-sánchez_sánchez_briones-moreno_vera-sirera_carrera_ripoll_yanofsky_et al._2018, title={Gibberellins negatively modulate ovule number in plants}, volume={145}, ISSN={1477-9129 0950-1991}, url={http://dx.doi.org/10.1242/dev.163865}, DOI={10.1242/dev.163865}, number={13}, journal={Development}, publisher={The Company of Biologists}, author={Gomez, M. D. and Barro-Trastoy, D. and Escoms, E. and Saura-Sánchez, M. and Sánchez, I. and Briones-Moreno, A. and Vera-Sirera, F. and Carrera, E. and Ripoll, J. J. and Yanofsky, M. F. and et al.}, year={2018}, month={Jan}, pages={dev163865} }
 @article{brumos_robles_yun_vu_jackson_alonso_stepanova_2018, title={Local Auxin Biosynthesis Is a Key Regulator of Plant Development}, volume={47}, DOI={10.1016/j.devcel.2018.09.022}, number={3}, journal={DEVELOPMENTAL CELL}, author={Brumos, Javier and Robles, Linda M. and Yun, Jeonga and Vu, Thien C. and Jackson, Savannah and Alonso, Jose and Stepanova, Anna N.}, year={2018}, pages={306-} }
 @article{yanagisawa_alonso_szymanski_2018, title={Microtubule-Dependent Confinement of a Cell Signaling and Actin Polymerization Control Module Regulates Polarized Cell Growth}, volume={28}, ISSN={0960-9822}, url={http://dx.doi.org/10.1016/J.CUB.2018.05.076}, DOI={10.1016/J.CUB.2018.05.076}, number={15}, journal={Current Biology}, publisher={Elsevier BV}, author={Yanagisawa, Makoto and Alonso, Jose M. and Szymanski, Daniel B.}, year={2018}, month={Aug}, pages={2459–2466.e4} }
 @article{estrada-johnson_csukasi_pizarro_vallarino_kiryakova_vioque_brumos_medina-escobar_botella_alonso_et al._2017, title={Transcriptomic analysis in strawberry fruits reveals active auxin biosynthesis and signaling in the ripe receptacle}, volume={8}, journal={Frontiers in Plant Science}, author={Estrada-Johnson, E. and Csukasi, F. and Pizarro, C. M. and Vallarino, J. G. and Kiryakova, Y. and Vioque, A. and Brumos, J. and Medina-Escobar, N. and Botella, M. A. and Alonso, J. M. and et al.}, year={2017} }
 @article{estrada-johnson_csukasi_pizarro_vallarino_kiryakova_vioque_merchante_brumos_medina-escobar_botella_et al._2017, title={Transcriptomic analysis in strawberry fruits reveals active auxin biosynthesis and signaling in the ripe receptacle (vol 8, pg 889, 2017)}, volume={8}, DOI={10.3389/fpls.2017.01305}, journal={Frontiers in Plant Science}, author={Estrada-Johnson, E. and Csukasi, F. and Pizarro, C. M. and Vallarino, J. G. and Kiryakova, Y. and Vioque, A. and Merchante, C. and Brumos, J. and Medina-Escobar, N. and Botella, M. A. and et al.}, year={2017} }
 @article{merchante_stepanova_alonso_2017, title={Translation regulation in plants: An interesting past, an exciting present and a promising future}, volume={90}, DOI={10.1111/tpj.13520}, number={4}, journal={Plant Journal}, author={Merchante, C. and Stepanova, A. N. and Alonso, Jose}, year={2017}, pages={628–653} }
 @book{merchante_yun_valpuesta-fernandez_stepanova_alonso_2017, title={Translation regulation of uORFs-containing genes in Arabidopsis}, author={Merchante, C. and Yun, J. and Valpuesta-Fernandez, V. and Stepanova, A. and Alonso, J.}, year={2017} }
 @misc{provart_alonso_assmann_bergmann_brady_brkljacic_browse_chapple_colot_cutler_et al._2016, title={50 years of Arabidopsis research: Highlights and future directions}, volume={209}, number={3}, journal={New Phytologist}, author={Provart, N. J. and Alonso, J. and Assmann, S. M. and Bergmann, D. and Brady, S. M. and Brkljacic, J. and Browse, J. and Chapple, C. and Colot, V. and Cutler, S. and et al.}, year={2016}, pages={921–944} }
 @article{merchante_hu_heber_alonso_stepanova_2016, title={A Ribosome Footprinting Protocol for Plants}, volume={6}, ISSN={2331-8325}, url={http://dx.doi.org/10.21769/bioprotoc.1985}, DOI={10.21769/bioprotoc.1985}, number={21}, journal={BIO-PROTOCOL}, publisher={Bio-Protocol, LLC}, author={Merchante, Catharina and Hu, Qiwen and Heber, Steffen and Alonso, Jose and Stepanova, Anna}, year={2016} }
 @article{stepanova_alonso_2016, title={Auxin catabolism unplugged: Role of IAA oxidation in auxin homeostasis}, volume={113}, DOI={10.1073/pnas.1613506113}, number={39}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Stepanova, A. N. and Alonso, Jose}, year={2016}, pages={10742–10744} }
 @article{stepanova_alonso_2016, title={Cutting out the middle man in light-hormone interactions}, volume={39}, DOI={10.1016/j.devcel.2016.11.013}, number={5}, journal={Developmental Cell}, author={Stepanova, A. N. and Alonso, Jose}, year={2016}, pages={524–526} }
 @article{hu_merchante_stepanova_alonso_heber_2016, title={Genome-wide search for translated upstream open reading frames in Arabidopsis thaliana}, volume={15}, number={2}, journal={IEEE Transactions on Nanobioscience}, author={Hu, Q. W. and Merchante, C. and Stepanova, A. N. and Alonso, J. M. and Heber, S.}, year={2016}, pages={150–159} }
 @book{merchante_brumós_yun_stepanova_alonso_2016, title={Hormone-Mediated Gene-Specific Translation Regulation}, url={http://hdl.handle.net/10630/11885}, author={Merchante, C. and Brumós, J. and Yun, J. and Stepanova, A. and Alonso, J.}, year={2016} }
 @article{alonso_stepanova_2015, title={A Recombineering-based gene tagging system for Arabidopsis}, volume={1227}, journal={Bacterial artificial chromosomes, 2nd edition}, author={Alonso, J. M. and Stepanova, A. N.}, year={2015}, pages={233–243} }
 @inbook{hu_merchante_stepanova_alonso_heber_2015, title={A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana}, ISBN={9783319190471 9783319190488}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/978-3-319-19048-8_12}, DOI={10.1007/978-3-319-19048-8_12}, booktitle={Bioinformatics Research and Applications}, publisher={Springer International Publishing}, author={Hu, Qiwen and Merchante, Catharina and Stepanova, Anna N. and Alonso, Jose M. and Heber, Steffen}, year={2015}, pages={138–149} }
 @inproceedings{hu_merchante_stepanova_alonso_heber_2015, title={A stacking-based approach to identify translated upstream open reading frames in Arabidopsis thaliana}, volume={9096}, booktitle={Bioinformatics research and applications (isbra 2015)}, author={Hu, Q. W. and Merchante, C. and Stepanova, A. N. and Alonso, J. M. and Heber, S.}, year={2015}, pages={138–149} }
 @article{fabregas_formosa-jordan_confraria_siligato_alonso_swarup_bennett_mahonen_cano-delgado_ibanes_2015, title={Auxin influx carriers control vascular patterning and xylem differentiation in Arabidopsis thaliana}, volume={11}, DOI={10.1371/journal.pgen.1005183}, number={4}, journal={PLoS Genetics}, author={Fabregas, N. and Formosa-Jordan, P. and Confraria, A. and Siligato, R. and Alonso, Jose and Swarup, R. and Bennett, M. J. and Mahonen, A. P. and Cano-Delgado, A. I. and Ibanes, M.}, year={2015} }
 @article{worden_wilkop_esteve_jeannotte_lathe_vernhettes_weimer_hicks_alonso_labavitch_et al._2015, title={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}, volume={167}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.114.249003}, DOI={10.1104/pp.114.249003}, number={2}, journal={Plant Physiology}, publisher={Oxford University Press (OUP)}, author={Worden, Natasha and Wilkop, Thomas E. and Esteve, Victor Esteva and Jeannotte, Richard and Lathe, Rahul and Vernhettes, Samantha and Weimer, Bart and Hicks, Glenn and Alonso, Jose and Labavitch, John and et al.}, year={2015}, month={Feb}, pages={381–393} }
 @article{merchante_brumos_yun_hu_spencer_enriquez_binder_heber_stepanova_alonso_2015, title={Gene-specific translation regulation mediated by the hormone-signaling molecule EIN2}, volume={163}, DOI={10.1016/j.cell.2015.09.036}, number={3}, journal={Cell}, author={Merchante, C. and Brumos, J. and Yun, J. and Hu, Q. W. and Spencer, K. R. and Enriquez, P. and Binder, B. M. and Heber, S. and Stepanova, A. N. and Alonso, Jose}, year={2015}, pages={684–697} }
 @inproceedings{hu_merchante_stepanova_alonso_heber_2015, title={Mining transcript features related to translation in Arabidopsis using LASSO and random forest}, DOI={10.1109/iccabs.2015.7344713}, booktitle={International conference on computational advances in bio and medical}, author={Hu, Q. W. and Merchante, C. and Stepanova, A. N. and Alonso, Jose and Heber, S.}, year={2015} }
 @article{alonso_stepanova_2015, title={Plant functional genomics methods and protocols second edition preface}, volume={1284}, journal={Plant functional genomics: methods and protocols, 2nd edition}, author={Alonso, J. M. and Stepanova, A. N.}, year={2015}, pages={V-} }
 @book{alonso_stepanova_2015, place={Humana Press}, edition={2nd}, series={Methods in Molecular Biology}, title={Plant functional genomics: Methods and protocols}, ISBN={9781493924431 9781493924448}, DOI={10.1007/978-1-4939-2444-8}, publisher={New York}, year={2015}, collection={Methods in Molecular Biology} }
 @article{han_alonso_rojas-pierce_2015, title={Regulator of bulb biogenesis1 (RBB1) is involved in vacuole bulb formation in arabidopsis}, volume={10}, DOI={10.1371/journal.pone.0125621}, number={4}, journal={PLoS One}, author={Han, S. W. and Alonso, Jose and Rojas-Pierce, Marcela}, year={2015} }
 @article{moreno-risueno_sozzani_yardimci_petricka_vernoux_blilou_alonso_winter_ohler_scheres_et al._2015, title={Transcriptional control of tissue formation throughout root development}, volume={350}, DOI={10.1126/science.aad1171}, number={6259}, journal={Science}, author={Moreno-Risueno, M. A. and Sozzani, R. and Yardimci, G. G. and Petricka, J. J. and Vernoux, T. and Blilou, I. and Alonso, Jose and Winter, C. M. and Ohler, U. and Scheres, B. and et al.}, year={2015}, pages={426–430} }
 @inbook{alonso_stepanova_2014, title={Arabidopsis Transformation with Large Bacterial Artificial Chromosomes}, booktitle={Arabidopsis Protocols}, author={Alonso, Jose M. and Stepanova, Anna N.}, year={2014}, pages={271–283} }
 @article{brumos_alonso_stepanova_2014, title={Genetic aspects of auxin biosynthesis and its regulation}, volume={151}, DOI={10.1111/ppl.12098}, number={1}, journal={Physiologia plantarum}, author={Brumos, Javier and Alonso, Jose and Stepanova, Anna N.}, year={2014}, pages={3–12} }
 @article{band_wells_fozard_ghetiu_french_pound_wilson_yu_li_hijazi_et al._2014, title={Systems analysis of auxin transport in the arabidopsis root apex}, volume={26}, number={3}, journal={Plant Cell}, author={Band, L. R. and Wells, D. M. and Fozard, J. A. and Ghetiu, T. and French, A. P. and Pound, M. P. and Wilson, M. H. and Yu, L. and Li, W. D. and Hijazi, H. I. and et al.}, year={2014}, pages={862–875} }
 @article{catalá_lópez-cobollo_mar castellano_angosto_alonso_ecker_salinas_2014, title={The Arabidopsis 14-3-3 Protein RARE COLD INDUCIBLE 1A Links Low-Temperature Response and Ethylene Biosynthesis to Regulate Freezing Tolerance and Cold Acclimation
 }, volume={26}, ISSN={1532-298X 1040-4651}, url={http://dx.doi.org/10.1105/tpc.114.127605}, DOI={10.1105/tpc.114.127605}, abstractNote={Abstract
               <jats:p>In plants, the expression of 14-3-3 genes reacts to various adverse environmental conditions, including cold, high salt, and drought. Although these results suggest that 14-3-3 proteins have the potential to regulate plant responses to abiotic stresses, their role in such responses remains poorly understood. Previously, we showed that the RARE COLD INDUCIBLE 1A (RCI1A) gene encodes the 14-3-3 psi isoform. Here, we present genetic and molecular evidence implicating RCI1A in the response to low temperature. Our results demonstrate that RCI1A functions as a negative regulator of constitutive freezing tolerance and cold acclimation in Arabidopsis thaliana by controlling cold-induced gene expression. Interestingly, this control is partially performed through an ethylene (ET)-dependent pathway involving physical interaction with different ACC SYNTHASE (ACS) isoforms and a decreased ACS stability. We show that, consequently, RCI1A restrains ET biosynthesis, contributing to establish adequate levels of this hormone in Arabidopsis under both standard and low-temperature conditions. We further show that these levels are required to promote proper cold-induced gene expression and freezing tolerance before and after cold acclimation. All these data indicate that RCI1A connects the low-temperature response with ET biosynthesis to modulate constitutive freezing tolerance and cold acclimation in Arabidopsis.}, number={8}, journal={The Plant Cell}, publisher={Oxford University Press (OUP)}, author={Catalá, Rafael and López-Cobollo, Rosa and Mar Castellano, M. and Angosto, Trinidad and Alonso, José M. and Ecker, Joseph R. and Salinas, Julio}, year={2014}, month={Aug}, pages={3326–3342} }
 @article{pietra_gustavsson_kiefer_kalmbach_hörstedt_ikeda_stepanova_alonso_grebe_2013, title={Arabidopsis SABRE and CLASP interact to stabilize cell division plane orientation and planar polarity}, volume={4}, DOI={10.1038/ncomms3779}, journal={Nature communications}, author={Pietra, Stefano and Gustavsson, Anna and Kiefer, Christian and Kalmbach, Lothar and Hörstedt, Per and Ikeda, Yoshihisa and Stepanova, Anna N. and Alonso, Jose and Grebe, Markus}, year={2013} }
 @article{merchante_alonso_stepanova_2013, title={Ethylene signaling: simple ligand, complex regulation}, volume={16}, DOI={10.1016/j.pbi.2013.08.001}, number={5}, journal={Current opinion in plant biology}, author={Merchante, Catharina and Alonso, Jose and Stepanova, Anna N.}, year={2013}, pages={554–560} }
 @article{hill_mathews_kim_street_wildes_chiang_mason_alonso_ecker_kieber_et al._2013, title={Functional Characterization of Type-B Response Regulators in the Arabidopsis Cytokinin Response
 
 }, volume={162}, ISSN={1532-2548}, url={http://dx.doi.org/10.1104/pp.112.208736}, DOI={10.1104/pp.112.208736}, number={1}, journal={Plant Physiology}, publisher={Oxford University Press (OUP)}, author={Hill, Kristine and Mathews, Dennis E. and Kim, Hyo Jung and Street, Ian H. and Wildes, Sarah L. and Chiang, Yi-Hsuan and Mason, Michael G. and Alonso, Jose M. and Ecker, Joseph R. and Kieber, Joseph J. and et al.}, year={2013}, month={May}, pages={212–224} }
 @article{kopycki_wieduwild_kohlschmidt_brandt_stepanova_alonso_pedras_abel_grubb_2013, title={Kinetic analysis of Arabidopsis glucosyltransferase UGT74B1 illustrates a general mechanism by which enzymes can escape product inhibition}, volume={450}, DOI={10.1042/bj20121403}, journal={Biochemical Journal (London, England : 1984)}, author={Kopycki, J. and Wieduwild, E. and Kohlschmidt, J. and Brandt, W. and Stepanova, A. N. and Alonso, Jose and Pedras, M. S. C. and Abel, S. and Grubb, C. D.}, year={2013}, pages={37–46} }
 @article{robert_grones_stepanova_robles_lokerse_alonso_weijers_friml_2013, title={Local Auxin Sources Orient the Apical-Basal Axis in< i> Arabidopsis</i> Embryos}, volume={23}, DOI={10.1016/j.cub.2013.09.039}, number={24}, journal={Current Biology}, author={Robert, Hélène S. and Grones, Peter and Stepanova, Anna N. and Robles, Linda M. and Lokerse, Annemarie S. and Alonso, Jose and Weijers, Dolf and Friml, Jiří}, year={2013}, pages={2506–2512} }
 @article{robles_stepanova_alonso_2013, title={Molecular mechanisms of ethyleneauxin interaction}, volume={6}, DOI={10.1093/mp/sst113}, number={6}, journal={Molecular Plant}, author={Robles, L. and Stepanova, A. and Alonso, J.}, year={2013}, pages={1734–1737} }
 @article{robles_stepanova_alonso_2013, title={Molecular mechanisms of ethylene–auxin interactions}, journal={Molecular plant}, author={Robles, Linda and Stepanova, Anna and Alonso, Jose}, year={2013}, pages={sst113} }
 @article{péret_swarup_ferguson_seth_yang_dhondt_james_casimiro_perry_syed_2012, title={AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during Arabidopsis development}, volume={24}, DOI={10.1105/tpc.112.097766}, number={7}, journal={The Plant Cell Online}, author={Péret, Benjamin and Swarup, Kamal and Ferguson, Alison and Seth, Malvika and Yang, Yaodong and Dhondt, Stijn and James, Nicholas and Casimiro, Ilda and Perry, Paula and Syed, Adnan}, year={2012}, pages={2874–2885} }
 @article{peret_swarup_ferguson_seth_yang_dhondt_james_casimiro_perry_syed_et al._2012, title={AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during arabidopsis development}, volume={24}, number={7}, journal={Plant Cell}, author={Peret, B. and Swarup, K. and Ferguson, A. and Seth, M. and Yang, Y. D. and Dhondt, S. and James, N. and Casimiro, I. and Perry, P. and Syed, A. and et al.}, year={2012}, pages={2874–2885} }
 @article{zhou_benavente_stepanova_alonso_2011, title={A recombineering‐based gene tagging system for Arabidopsis}, volume={66}, DOI={10.1111/j.1365-313x.2011.04524.x}, number={4}, journal={The Plant Journal}, author={Zhou, Rongrong and Benavente, Larissa M. and Stepanova, Anna N. and Alonso, Jose M.}, year={2011}, pages={712–723} }
 @article{he_brumos_li_ji_ke_gong_zeng_li_zhang_an_et al._2011, title={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}, volume={23}, DOI={10.1105/tpc.111.089029}, number={11}, journal={The Plant Cell Online}, author={He, W. R. and Brumos, J. and Li, H. J. and Ji, Y. S. and Ke, M. and Gong, X. Q. and Zeng, Q. L. and Li, W. Y. and Zhang, X. Y. and An, F. Y. and et al.}, year={2011}, pages={3944–3960} }
 @article{stepanova_alonso_2011, title={Bypassing transcription: a shortcut in cytokinin-auxin interactions}, volume={21}, DOI={10.1016/j.devcel.2011.09.016}, number={4}, journal={Developmental cell}, author={Stepanova, Anna N. and Alonso, Jose}, year={2011}, pages={608–610} }
 @article{stepanova_yun_robles_novak_he_guo_ljung_alonso_2011, title={The Arabidopsis YUCCA1 flavin monooxygenase functions in the indole-3-pyruvic acid branch of auxin biosynthesis}, volume={23}, DOI={10.1105/tpc.111.088047}, number={11}, journal={The Plant Cell Online}, author={Stepanova, Anna N. and Yun, Jeonga and Robles, Linda M. and Novak, Ondrej and He, Wenrong and Guo, Hongwei and Ljung, Karin and Alonso, Jose}, year={2011}, pages={3961–3973} }
 @article{tsuchisaka_yu_jin_alonso_ecker_zhang_gao_theologis_2009, title={A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana}, volume={183}, DOI={10.1534/genetics.109.107102}, number={3}, journal={Genetics}, author={Tsuchisaka, Atsunari and Yu, Guixia and Jin, Hailing and Alonso, Jose M. and Ecker, Joseph R. and Zhang, Xiaoming and Gao, Shang and Theologis, Athanasios}, year={2009}, pages={979–1003} }
 @article{stepanova_alonso_2009, title={Ethylene signaling and response: where different regulatory modules meet}, volume={12}, DOI={10.1016/j.pbi.2009.07.009}, number={5}, journal={Current opinion in plant biology}, author={Stepanova, Anna N. and Alonso, Jose}, year={2009}, pages={548–555} }
 @article{ikeda_men_fischer_stepanova_alonso_ljung_grebe_2009, title={Local auxin biosynthesis modulates gradient-directed planar polarity in Arabidopsis}, volume={11}, DOI={10.1038/ncb1879}, number={6}, journal={Nature Cell Biology}, author={Ikeda, Yoshihisa and Men, Shuzhen and Fischer, Urs and Stepanova, Anna N. and Alonso, José M. and Ljung, Karin and Grebe, Markus}, year={2009}, pages={731–738} }
 @article{stepanova_robertson-hoyt_yun_benavente_xie_doležal_schlereth_jürgens_alonso_2008, title={< i> TAA1</i>-Mediated Auxin Biosynthesis Is Essential for Hormone Crosstalk and Plant Development}, volume={133}, DOI={10.1016/j.cell.2008.01.047}, number={1}, journal={Cell}, author={Stepanova, Anna N. and Robertson-Hoyt, Joyce and Yun, Jeonga and Benavente, Larissa M. and Xie, De-Yu and Doležal, Karel and Schlereth, Alexandra and Jürgens, Gerd and Alonso, Jose}, year={2008}, pages={177–191} }
 @article{hu_mitchum_barnaby_ayele_ogawa_nam_lai_hanada_alonso_ecker_2008, title={Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis}, volume={20}, DOI={10.1105/tpc.107.057752}, number={2}, journal={The Plant Cell Online}, author={Hu, Jianhong and Mitchum, Melissa G. and Barnaby, Neel and Ayele, Belay T. and Ogawa, Mikihiro and Nam, Edward and Lai, Wei-Chu and Hanada, Atsushi and Alonso, Jose M. and Ecker, Joseph R.}, year={2008}, pages={320–336} }
 @article{leivar_monte_al-sady_carle_storer_alonso_ecker_quail_2008, title={The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels}, volume={20}, DOI={10.1105/tpc.107.052142}, number={2}, journal={The Plant Cell Online}, author={Leivar, Pablo and Monte, Elena and Al-Sady, Bassem and Carle, Christine and Storer, Alyssa and Alonso, Jose M. and Ecker, Joseph R. and Quail, Peter H.}, year={2008}, pages={337–352} }
 @article{li_he_lu_lee_alonso_ecker_luan_2007, title={A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis}, volume={19}, DOI={10.1105/tpc.107.053579}, number={8}, journal={The Plant Cell Online}, author={Li, Hong and He, Zengyong and Lu, Guihua and Lee, Sung Chul and Alonso, Jose and Ecker, Joseph R. and Luan, Sheng}, year={2007}, pages={2403–2416} }
 @article{o’malley_alonso_kim_leisse_ecker_2007, title={An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome}, volume={2}, DOI={10.1038/nprot.2007.425}, number={11}, journal={Nature protocols}, author={O’Malley, Ronan C. and Alonso, Jose and Kim, Christopher J. and Leisse, Thomas J. and Ecker, Joseph R.}, year={2007}, pages={2910–2917} }
 @article{chekanova_gregory_reverdatto_chen_kumar_hooker_yazaki_li_skiba_peng_2007, title={Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the< i> Arabidopsis</i> Transcriptome}, volume={131}, DOI={10.1016/j.cell.2007.10.056}, number={7}, journal={Cell}, author={Chekanova, Julia A. and Gregory, Brian D. and Reverdatto, Sergei V. and Chen, Huaming and Kumar, Ravi and Hooker, Tanya and Yazaki, Junshi and Li, Pinghua and Skiba, Nikolai and Peng, Qian}, year={2007}, pages={1340–1353} }
 @article{stepanova_yun_likhacheva_alonso_2007, title={Multilevel interactions between ethylene and auxin in Arabidopsis roots}, volume={19}, DOI={10.1105/tpc.107.052068}, number={7}, journal={The Plant Cell Online}, author={Stepanova, Anna N. and Yun, Jeonga and Likhacheva, Alla V. and Alonso, Jose}, year={2007}, pages={2169–2185} }
 @article{mori_murata_yang_munemasa_wang_andreoli_tiriac_alonso_harper_ecker_2006, title={CDPKs CPK6 and CPK3 function in ABA regulation of guard cell S-type anion-and Ca2+-permeable channels and stomatal closure}, volume={4}, number={10}, journal={PLoS biology}, author={Mori, Izumi C. and Murata, Yoshiyuki and Yang, Yingzhen and Munemasa, Shintaro and Wang, Yong-Fei and Andreoli, Shannon and Tiriac, Hervé and Alonso, Jose M. and Harper, Jeffery F. and Ecker, Joseph R.}, year={2006}, pages={e327} }
 @article{rudella_friso_alonso_ecker_wijk_2006, title={Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis}, volume={18}, DOI={10.1105/tpc.106.042861}, number={7}, journal={The Plant Cell Online}, author={Rudella, Andrea and Friso, Giulia and Alonso, Jose and Ecker, Joseph R. and Wijk, Klaas J. Van}, year={2006}, pages={1704–1721} }
 @article{kim_punshon_lanzirotti_li_alonso_ecker_kaplan_guerinot_2006, title={Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1}, volume={314}, DOI={10.1126/science.1132563}, number={5803}, journal={Science}, author={Kim, Sun A. and Punshon, Tracy and Lanzirotti, Antonio and Li, Liangtao and Alonso, José M. and Ecker, Joseph R. and Kaplan, Jerry and Guerinot, Mary Lou}, year={2006}, pages={1295–1298} }
 @article{benavente_alonso_2006, title={Molecular mechanisms of ethylene signaling in Arabidopsis}, volume={2}, ISSN={1742-206X 1742-2051}, url={http://dx.doi.org/10.1039/b513874d}, DOI={10.1039/b513874d}, number={3-4}, journal={Molecular BioSystems}, publisher={Royal Society of Chemistry (RSC)}, author={Benavente, Larissa M. and Alonso, Jose M.}, year={2006}, pages={165} }
 @article{alonso_ecker_2006, title={Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis}, volume={7}, DOI={10.1038/nrg1893}, number={7}, journal={Nature Reviews Genetics}, author={Alonso, Jose and Ecker, Joseph R.}, year={2006}, pages={524–536} }
 @inbook{stepanova_alonso_2006, title={PCR-based screening for insertional mutants}, booktitle={Arabidopsis Protocols}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2006}, pages={163–172} }
 @article{lariguet_schepens_hodgson_pedmale_trevisan_kami_carbonnel_alonso_ecker_liscum_2006, title={PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism}, volume={103}, DOI={10.1073/pnas.0603799103}, number={26}, journal={Proceedings of the National Academy of Sciences}, author={Lariguet, Patricia and Schepens, Isabelle and Hodgson, Daniel and Pedmale, Ullas V. and Trevisan, Martine and Kami, Chitose and Carbonnel, Matthieu and Alonso, José M. and Ecker, Joseph R. and Liscum, Emmanuel}, year={2006}, pages={10134–10139} }
 @article{chen_ullah_temple_liang_guo_alonso_ecker_jones_2006, title={RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis}, volume={57}, DOI={10.1093/jxb/erl035}, number={11}, journal={Journal of experimental botany}, author={Chen, Jin-Gui and Ullah, Hemayet and Temple, Brenda and Liang, Jiansheng and Guo, Jianjun and Alonso, José M. and Ecker, Joseph R. and Jones, Alan M.}, year={2006}, pages={2697–2708} }
 @article{hutchison_li_argueso_gonzalez_lee_lewis_maxwell_perdue_schaller_alonso_2006, title={The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling}, volume={18}, DOI={10.1105/tpc.106.045674}, number={11}, journal={The Plant Cell Online}, author={Hutchison, Claire E. and Li, Jie and Argueso, Cristiana and Gonzalez, Monica and Lee, Eurie and Lewis, Michael W. and Maxwell, Bridey B. and Perdue, Tony D. and Schaller, G. Eric and Alonso, Jose M.}, year={2006}, pages={3073–3087} }
 @article{pfund_tans-kersten_dunning_alonso_ecker_allen_bent_2005, title={" Flagellin is not a major defense elicitor in Ralstonia solanacearum cells (vol 17, pg 696, 2005)}, volume={18}, number={9}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Pfund, C. and Tans-Kersten, J. and Dunning, F. M. and Alonso, J. M. and Ecker, J. R. and Allen, C. and Bent, A. F.}, year={2005}, pages={1024} }
 @article{stepanova_hoyt_hamilton_alonso_2005, title={A link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis}, volume={17}, ISBN={1040-4651}, DOI={10.1105/tpc.105.033365}, number={8}, journal={The Plant Cell Online}, author={Stepanova, Anna N. and Hoyt, Joyce M. and Hamilton, Alexandra A. and Alonso, Jose M.}, year={2005}, pages={2230–2242} }
 @article{liu_holub_alonso_ecker_fobert_2005, title={An Arabidopsis NPR1‐like gene, NPR4, is required for disease resistance}, volume={41}, DOI={10.1111/j.1365-313x.2004.02296.x}, number={2}, journal={The Plant Journal}, author={Liu, Guosheng and Holub, Eric B. and Alonso, Jose M. and Ecker, Joseph R. and Fobert, Pierre R.}, year={2005}, pages={304–318} }
 @article{stepanova_alonso_2005, title={Arabidopsis ethylene signaling pathway}, volume={2005}, number={276}, journal={Science Signaling}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2005}, pages={cm4} }
 @article{nagpal_ellis_weber_ploense_barkawi_guilfoyle_hagen_alonso_cohen_farmer_2005, title={Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation}, volume={132}, number={18}, journal={Development}, author={Nagpal, Punita and Ellis, Christine M. and Weber, Hans and Ploense, Sara E. and Barkawi, Lana S. and Guilfoyle, Thomas J. and Hagen, Gretchen and Alonso, José M. and Cohen, Jerry D. and Farmer, Edward E.}, year={2005}, pages={4107–4118} }
 @article{prigge_otsuga_alonso_ecker_drews_clark_2005, title={Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development}, volume={17}, number={1}, journal={The Plant Cell Online}, author={Prigge, Michael J. and Otsuga, Denichiro and Alonso, Jose M. and Ecker, Joseph R. and Drews, Gary N. and Clark, Steven E.}, year={2005}, pages={61–76} }
 @article{stepanova_alonso_2005, title={Ethylene signalling and response pathway: a unique signalling cascade with a multitude of inputs and outputs}, volume={123}, DOI={10.1111/j/1399-3054.2004.00447}, number={2}, journal={Physiologia Plantarum}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2005}, pages={195–206} }
 @article{okushima_overvoorde_arima_alonso_chan_chang_ecker_hughes_lui_nguyen_2005, title={Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19}, volume={17}, number={2}, journal={The Plant Cell Online}, author={Okushima, Yoko and Overvoorde, Paul J. and Arima, Kazunari and Alonso, Jose M. and Chan, April and Chang, Charlie and Ecker, Joseph R. and Hughes, Beth and Lui, Amy and Nguyen, Diana}, year={2005}, pages={444–463} }
 @article{overvoorde_okushima_alonso_chan_chang_ecker_hughes_liu_onodera_quach_2005, title={Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana}, volume={17}, number={12}, journal={The Plant Cell Online}, author={Overvoorde, Paul J. and Okushima, Yoko and Alonso, José M. and Chan, April and Chang, Charlie and Ecker, Joseph R. and Hughes, Beth and Liu, Amy and Onodera, Courtney and Quach, Hong}, year={2005}, pages={3282–3300} }
 @article{mason_mathews_argyros_maxwell_kieber_alonso_ecker_schaller_2005, title={Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis}, volume={17}, number={11}, journal={The Plant Cell Online}, author={Mason, Michael G. and Mathews, Dennis E. and Argyros, D. Aaron and Maxwell, Bridey B. and Kieber, Joseph J. and Alonso, Jose M. and Ecker, Joseph R. and Schaller, G. Eric}, year={2005}, pages={3007–3018} }
 @article{wilmoth_wang_tiwari_joshi_hagen_guilfoyle_alonso_ecker_reed_2005, title={NPH4/ARF7 and ARF19 promote leaf expansion and auxin‐induced lateral root formation}, volume={43}, number={1}, journal={The Plant Journal}, author={Wilmoth, Jill C. and Wang, Shucai and Tiwari, Shiv B. and Joshi, Atul D. and Hagen, Gretchen and Guilfoyle, Thomas J. and Alonso, Jose M. and Ecker, Joseph R. and Reed, Jason W.}, year={2005}, pages={118–130} }
 @article{ryu_kim_kunkel_kim_cho_hong_kim_fernández_kim_alonso_et al._2005, title={Phytochrome-Specific Type 5 Phosphatase Controls Light Signal Flux by Enhancing Phytochrome Stability and Affinity for a Signal Transducer}, volume={120}, ISSN={0092-8674}, url={http://dx.doi.org/10.1016/j.cell.2004.12.019}, DOI={10.1016/j.cell.2004.12.019}, number={3}, journal={Cell}, publisher={Elsevier BV}, author={Ryu, Jong Sang and Kim, Jeong-Il and Kunkel, Tim and Kim, Byung Chul and Cho, Dae Shik and Hong, Sung Hyun and Kim, Seong-Hee and Fernández, Aurora Piñas and Kim, Yumi and Alonso, Jose M. and et al.}, year={2005}, month={Feb}, pages={395–406} }
 @article{ryu_kim_kunkel_kim_cho_hong_kim_fernández_kim_alonso_2005, title={Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer}, volume={120}, number={3}, journal={Cell}, author={Ryu, Jong Sang and Kim, Jeong-Il and Kunkel, Tim and Kim, Byung Chul and Cho, Dae Shik and Hong, Sung Hyun and Kim, Seong-Hee and Fernández, Aurora Piñas and Kim, Yumi and Alonso, Jose M.}, year={2005}, pages={395–406} }
 @article{page_hamel_gabilly_zegzouti_perea_alonso_ecker_theg_christensen_merchant_2004, title={A Homolog of Prokaryotic Thiol Disulfide Transporter CcdA Is Required for the Assembly of the Cytochrome b6f Complex in Arabidopsis Chloroplasts}, volume={279}, ISSN={0021-9258 1083-351X}, url={http://dx.doi.org/10.1074/JBC.M404285200}, DOI={10.1074/JBC.M404285200}, number={31}, journal={Journal of Biological Chemistry}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Page, M. L. Dudley and Hamel, Patrice P. and Gabilly, Stéphane T. and Zegzouti, Hicham and Perea, John V. and Alonso, José M. and Ecker, Joseph R. and Theg, Steven M. and Christensen, Sioux K. and Merchant, Sabeeha}, year={2004}, month={May}, pages={32474–32482} }
 @article{novillo_alonso_ecker_salinas_2004, title={CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis}, volume={101}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.0303029101}, DOI={10.1073/PNAS.0303029101}, number={11}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Novillo, F. and Alonso, J. M. and Ecker, J. R. and Salinas, J.}, year={2004}, month={Mar}, pages={3985–3990} }
 @article{li_johnson_stepanova_alonso_ecker_2004, title={Convergence of Signaling Pathways in the Control of Differential Cell Growth in< i> Arabidopsis</i>}, volume={7}, number={2}, journal={Developmental cell}, author={Li, Hai and Johnson, Phoebe and Stepanova, Anna and Alonso, Jose M. and Ecker, Joseph R.}, year={2004}, pages={193–204} }
 @article{li_johnson_stepanova_alonso_ecker_2004, title={Convergence of signaling of differential cell growth pathways in the control in Arabidopsis}, volume={7}, DOI={10.1016/j.devcel.2004.07.002}, number={2}, journal={Developmental Cell}, author={Li, H. and Johnson, P. and Stepanova, A. and Alonso, J. M. and Ecker, J. R.}, year={2004}, pages={193–204} }
 @article{tyler_thomas_hu_dill_alonso_ecker_sun_2004, title={DELLA proteins and gibberellin-regulated seed germination and floral development in Arabidopsis}, volume={135}, number={2}, journal={Plant Physiology}, author={Tyler, Ludmila and Thomas, Stephen G. and Hu, Jianhong and Dill, Alyssa and Alonso, Jose M. and Ecker, Joseph R. and Sun, Tai-ping}, year={2004}, pages={1008–1019} }
 @article{pfund_tans-kersten_dunning_alonso_ecker_allen_bent_2004, title={Flagellin is not a major defense elicitor in Ralstonia solanacearum cells or extracts applied to Arabidopsis thaliana}, volume={17}, DOI={10.1094/MPMI.2004.17.6.696}, number={6}, journal={Molecular plant-microbe interactions}, author={Pfund, Christine and Tans-Kersten, Julie and Dunning, F. Mark and Alonso, Jose M. and Ecker, Joseph R. and Allen, Caitilyn and Bent, Andrew F.}, year={2004}, pages={696–706} }
 @article{chen_pandey_huang_alonso_ecker_assmann_jones_2004, title={GCR1 can act independently of heterotrimeric G-protein in response to brassinosteroids and gibberellins in Arabidopsis seed germination}, volume={135}, number={2}, journal={Plant Physiology}, author={Chen, Jin-Gui and Pandey, Sona and Huang, Jirong and Alonso, José M. and Ecker, Joseph R. and Assmann, Sarah M. and Jones, Alan M.}, year={2004}, pages={907–915} }
 @article{mockler_yu_shalitin_parikh_michael_liou_huang_smith_alonso_ecker_et al._2004, title={Regulation of flowering time in Arabidopsis by K homology domain proteins}, volume={101}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.0404552101}, DOI={10.1073/PNAS.0404552101}, number={34}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Mockler, T. C. and Yu, X. and Shalitin, D. and Parikh, D. and Michael, T. P. and Liou, J. and Huang, J. and Smith, Z. and Alonso, J. M. and Ecker, J. R. and et al.}, year={2004}, month={Aug}, pages={12759–12764} }
 @article{stepanova_alonso_2004, title={The canonical ethylene signaling pathway}, volume={2004}, number={221}, journal={Science Signaling}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2004}, pages={cm1} }
 @article{alonso_stepanova_2004, title={The ethylene signaling pathway}, volume={306}, DOI={10.1126/science.1104812}, number={5701}, journal={Science}, author={Alonso, Jose M. and Stepanova, Anna N.}, year={2004}, pages={1513–1515} }
 @article{monte_tepperman_al-sady_kaczorowski_alonso_ecker_li_zhang_quail_2004, title={The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development}, volume={101}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.0407107101}, DOI={10.1073/pnas.0407107101}, number={46}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Monte, E. and Tepperman, J. M. and Al-Sady, B. and Kaczorowski, K. A. and Alonso, J. M. and Ecker, J. R. and Li, X. and Zhang, Y. and Quail, P. H.}, year={2004}, month={Oct}, pages={16091–16098} }
 @article{to_haberer_ferreira_deruère_mason_schaller_alonso_ecker_kieber_2004, title={Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling}, volume={16}, number={3}, journal={The Plant Cell Online}, author={To, Jennifer P. C. and Haberer, Georg and Ferreira, Fernando J. and Deruère, Jean and Mason, Michael G. and Schaller, G. Eric and Alonso, Jose M. and Ecker, Joseph R. and Kieber, Joseph J.}, year={2004}, pages={658–671} }
 @article{mackey_belkhadir_alonso_ecker_dangl_2003, title={< i> Arabidopsis</i> RIN4 Is a Target of the Type III Virulence Effector AvrRpt2 and Modulates RPS2-Mediated Resistance}, volume={112}, number={3}, journal={Cell}, author={Mackey, David and Belkhadir, Youssef and Alonso, Jose M. and Ecker, Joseph R. and Dangl, Jeffery L.}, year={2003}, pages={379–389} }
 @article{lariguet_boccalandro_alonso_ecker_chory_casal_fankhauser_2003, title={A growth regulatory loop that provides homeostasis to phytochrome A signaling}, volume={15}, number={12}, journal={The Plant Cell Online}, author={Lariguet, Patricia and Boccalandro, Hernan E. and Alonso, José M. and Ecker, Joseph R. and Chory, Joanne and Casal, Jorge J. and Fankhauser, Christian}, year={2003}, pages={2966–2978} }
 @article{strand_asami_alonso_ecker_chory_2003, title={Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX}, volume={421}, number={6918}, journal={Nature}, author={Strand, Åsa and Asami, Tadao and Alonso, Jose and Ecker, Joseph R. and Chory, Joanne}, year={2003}, pages={79–83} }
 @article{michael_salome_hannah_spencer_sharp_mcpeek_alonso_ecker_mcclung_2003, title={Enhanced fitness conferred by naturally occurring variation in the circadian clock}, volume={302}, number={5647}, journal={Science}, author={Michael, Todd P. and Salome, Patrice A. and Hannah, J. Yu and Spencer, Taylor R. and Sharp, Emily L. and McPeek, Mark A. and Alonso, Jose M. and Ecker, Joseph R. and McClung, C. Robertson}, year={2003}, pages={1049–1053} }
 @article{alonso_stepanova_solano_wisman_ferrari_ausubel_ecker_2003, title={Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis}, volume={100}, number={5}, journal={Proceedings of the National Academy of Sciences}, author={Alonso, Jose M. and Stepanova, Anna N. and Solano, Roberto and Wisman, Ellen and Ferrari, Simone and Ausubel, Frederick M. and Ecker, Joseph R.}, year={2003}, pages={2992–2997} }
 @article{larkin_alonso_ecker_chory_2003, title={GUN4, a regulator of chlorophyll synthesis and intracellular signaling}, volume={299}, number={5608}, journal={Science}, author={Larkin, Robert M. and Alonso, Jose M. and Ecker, Joseph R. and Chory, Joanne}, year={2003}, pages={902–906} }
 @article{alonso_stepanova_leisse_kim_chen_shinn_stevenson_zimmerman_barajas_cheuk_2003, title={Genome-wide insertional mutagenesis of Arabidopsis thaliana}, volume={301}, number={5633}, journal={Science}, author={Alonso, Jose M. and Stepanova, Anna N. and Leisse, Thomas J. and Kim, Christopher J. and Chen, Huaming and Shinn, Paul and Stevenson, Denise K. and Zimmerman, Justin and Barajas, Pascual and Cheuk, Rosa}, year={2003}, pages={653–657} }
 @article{alonso_2003, title={Genome-wide insertional mutagenesis of Arabidopsis thaliana (vol 301, pg 653, 2003)}, volume={301}, number={5641}, journal={Science}, author={Alonso, J. M.}, year={2003}, pages={1849} }
 @article{monte_alonso_ecker_zhang_li_young_austin-phillips_quail_2003, title={Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways}, volume={15}, number={9}, journal={The Plant Cell Online}, author={Monte, Elena and Alonso, José M. and Ecker, Joseph R. and Zhang, Yuelin and Li, Xin and Young, Jeff and Austin-Phillips, Sandra and Quail, Peter H.}, year={2003}, pages={1962–1980} }
 @article{catalá_santos_alonso_ecker_martínez-zapater_salinas_2003, title={Mutations in the Ca2+/H+ transporter CAX1 increase CBF/DREB1 expression and the cold-acclimation response in Arabidopsis}, volume={15}, number={12}, journal={The Plant Cell Online}, author={Catalá, Rafael and Santos, Elisa and Alonso, José M. and Ecker, Joseph R. and Martínez-Zapater, José M. and Salinas, Julio}, year={2003}, pages={2940–2951} }
 @inbook{alonso_stepanova_2003, title={T-DNA mutagenesis in Arabidopsis}, ISBN={1588291456}, DOI={10.1385/1-59259-413-1:177}, booktitle={Plant Functional Genomics}, author={Alonso, Jose M. and Stepanova, Anna N.}, year={2003}, pages={177–187} }
 @article{lariguet_boccalandro_alonso_ecker_chory_casal_fankhausera_2003, title={The Balance between phytochrome kinase substrate1 and PKS2 Provides Homeostasis for Phytochrome A Signaling in Arabidopsis}, journal={The Plant Cell Online}, author={Lariguet, Patricia and Boccalandro, Hernan E. and Alonso, José M. and Ecker, Joseph R. and Chory, Joanne and Casal, Jorge J. and Fankhausera, Christian}, year={2003} }
 @article{ullah_chen_temple_boyes_alonso_davis_ecker_jones_2003, title={The β-subunit of the Arabidopsis G protein negatively regulates auxin-induced cell division and affects multiple developmental processes}, volume={15}, number={2}, journal={The Plant Cell Online}, author={Ullah, Hemayet and Chen, Jin-Gui and Temple, Brenda and Boyes, Douglas C. and Alonso, José M. and Davis, Keith R. and Ecker, Joseph R. and Jones, Alan M.}, year={2003}, pages={393–409} }
 @article{hu_aguirre_peto_alonso_ecker_chory_2002, title={A role for peroxisomes in photomorphogenesis and development of Arabidopsis}, volume={297}, number={5580}, journal={Science}, author={Hu, Jianping and Aguirre, Maria and Peto, Charles and Alonso, José and Ecker, Joseph and Chory, Joanne}, year={2002}, pages={405–409} }
 @article{schroeder_gahrtz_maxwell_cook_kan_alonso_ecker_chory_2002, title={De-Etiolated 1 and Damaged DNA Binding Protein 1 Interact to Regulate< i> Arabidopsis</i> Photomorphogenesis}, volume={12}, number={17}, journal={Current Biology}, author={Schroeder, Dana F. and Gahrtz, Manfred and Maxwell, Bridey B. and Cook, R. Kimberley and Kan, Jack M. and Alonso, José M. and Ecker, Joseph R. and Chory, Joanne}, year={2002}, pages={1462–1472} }
 @article{zheng_bednarek_sanderfoot_alonso_ecker_raikhel_2002, title={NPSN11 is a cell plate-associated SNARE protein that interacts with the syntaxin KNOLLE}, volume={129}, number={2}, journal={Plant physiology}, author={Zheng, Haiyan and Bednarek, Sebastian Y. and Sanderfoot, Anton A. and Alonso, Jose and Ecker, Joseph R. and Raikhel, Natasha V.}, year={2002}, pages={530–539} }
 @article{friedrichsen_nemhauser_muramitsu_maloof_alonso_ecker_furuya_chory_2002, title={Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth}, volume={162}, number={3}, journal={Genetics}, author={Friedrichsen, Danielle M. and Nemhauser, Jennifer and Muramitsu, Takamichi and Maloof, Julin N. and Alonso, José and Ecker, Joseph R. and Furuya, Masaki and Chory, Joanne}, year={2002}, pages={1445–1456} }
 @article{zhao_hull_gupta_goss_alonso_ecker_normanly_chory_celenza_2002, title={Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3}, volume={16}, number={23}, journal={Genes & Development}, author={Zhao, Yunde and Hull, Anna K. and Gupta, Neeru R. and Goss, Kendrick A. and Alonso, José and Ecker, Joseph R. and Normanly, Jennifer and Chory, Joanne and Celenza, John L.}, year={2002}, pages={3100–3112} }
 @article{jarillo_capel_tang_yang_alonso_ecker_cashmore_2001, title={An Arabidopsis circadian clock component interacts with both CRY1 and phyB}, volume={410}, number={6827}, journal={Nature}, author={Jarillo, Jose A. and Capel, Juan and Tang, Ru-Hang and Yang, Hong-Quan and Alonso, Jose M. and Ecker, Joseph R. and Cashmore, Anthony R.}, year={2001}, pages={487–490} }
 @article{jarillo_gabrys_capel_alonso_ecker_cashmore_2001, title={Phototropin-related NPL1 controls chloroplast relocation induced by blue light}, volume={410}, number={6831}, journal={Nature}, author={Jarillo, Jose A. and Gabrys, Halina and Capel, Juan and Alonso, Jose M. and Ecker, Joseph R. and Cashmore, Anthony R.}, year={2001}, pages={952–954} }
 @article{alonso_ecker_2001, title={The ethylene pathway: a paradigm for plant hormone signaling and interaction}, volume={2001}, number={70}, journal={Science Signaling}, author={Alonso, Jose M. and Ecker, Joseph R.}, year={2001}, pages={re1} }
 @article{hirayama_alonso_2000, title={Ethylene captures a metal! Metal ions are involved in ethylene perception and signal transduction}, volume={41}, number={5}, journal={Plant and Cell Physiology}, author={Hirayama, Takashi and Alonso, Jose M.}, year={2000}, pages={548–555} }
 @article{curie_alonso_le jean_ecker_briat_2000, title={Involvement of NRAMP1 from Arabidopsis thaliana in iron transport}, volume={347}, DOI={10.1042/0264-6021:3470749}, journal={Biochem. J}, author={Curie, Catherine and Alonso, J. and Le Jean, Marie and Ecker, J. and Briat, J.}, year={2000}, pages={749–755} }
 @article{theologis_ecker_palm_federspiel_kaul_white_alonso_altafi_araujo_bowman_2000, title={Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana}, volume={408}, number={6814}, journal={Nature}, author={Theologis, Athanasios and Ecker, Joseph R. and Palm, Curtis J. and Federspiel, Nancy A. and Kaul, Samir and White, Owen and Alonso, Jose and Altafi, Hootan and Araujo, Rina and Bowman, Cheryl L.}, year={2000}, pages={816–820} }
 @article{alonso_hirayama_roman_nourizadeh_ecker_1999, title={EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis}, volume={284}, number={5423}, journal={Science}, author={Alonso, Jose M. and Hirayama, Takashi and Roman, Gregg and Nourizadeh, Saeid and Ecker, Joseph R.}, year={1999}, pages={2148–2152} }
 @inbook{cubells-martinez_alonso_sanchez-ballesta_granell_1999, title={Ethylene Perception and Response in Citrus Fruit}, booktitle={Biology and Biotechnology of the Plant Hormone Ethylene II}, author={Cubells-Martinez, X. and Alonso, J. M. and Sanchez-Ballesta, M. T. and Granell, A.}, year={1999}, pages={137–143} }
 @article{hirayama_kieber_hirayama_kogan_guzman_nourizadeh_alonso_dailey_dancis_ecker_1999, title={RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson Disease–Related Copper Transporter, Is Required for Ethylene Signaling in< i> Arabidopsis</i>}, volume={97}, number={3}, journal={Cell}, author={Hirayama, Takashi and Kieber, Joseph J. and Hirayama, Noriko and Kogan, Mikhail and Guzman, Plinio and Nourizadeh, Saeid and Alonso, Jose M. and Dailey, William P. and Dancis, Andrew and Ecker, Joseph R.}, year={1999}, pages={383–393} }
 @article{alonso_chamarro_granell_1995, title={A non-photosynthetic ferredoxin gene is induced by ethylene in Citrus organs}, volume={29}, number={6}, journal={Plant molecular biology}, author={Alonso, José Miguel and Chamarro, Jesús and Granell, Antonio}, year={1995}, pages={1211–1221} }
 @article{alonso_granell_1995, title={A putative vacuolar processing protease is regulated by ethylene and also during fruit ripening in Citrus fruit}, volume={109}, number={2}, journal={Plant Physiology}, author={Alonso, Jose Miguel and Granell, Antonio}, year={1995}, pages={541–547} }
 @article{alonso_chamarro_granell_1995, title={Evidence for the involvement of ethylene in the expression of specific RNAs during maturation of the orange, a non-climacteric fruit}, volume={29}, number={2}, journal={Plant molecular biology}, author={Alonso, Jose Miguel and Chamarro, Jesús and Granell, Antonio}, year={1995}, pages={385–390} }
 @article{alonso_garcía‐martínez_chamarro_1992, title={Two dimensional gel electrophoresis patterns of total, in vivo labelled and in vitro translated polypeptides from orange flavedo during maturation and following ethylene treatment}, volume={85}, number={2}, journal={Physiologia Plantarum}, author={Alonso, José Miguel and García‐Martínez, José Luis and Chamarro, Jesús}, year={1992}, pages={147–156} }
 @inproceedings{merchante_hu_stepanova_alonso_heber, title={Deep sequencing of ribosomal footprints for studying genome-wide mRNA translation in plants}, author={Merchante, Karen and Hu, Qiwen and Stepanova, Anna N. and Alonso, Jose M. and Heber, Steffen} }