Anna Stepanova

Fernandez-Moreno, J.-P., Yaschenko, A. E., Neubauer, M., Marchi, A. J., Zhao, C., Ascencio-Ibanez, J. T., … Stepanova, A. N. (2024, February 21). A rapid and scalable approach to build synthetic repetitive hormone-responsive promoters. PLANT BIOTECHNOLOGY JOURNAL, Vol. 2. https://doi.org/10.1111/pbi.14313

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

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

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

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

Friesner, J., Colon-Carmona, A., Schnoes, A. M., Stepanova, A., Mason, G. A., Macintosh, G. C., … Dinneny, J. R. (2021). Broadening the impact of plant science through innovative, integrative, and inclusive outreach. PLANT DIRECT, 5(4). https://doi.org/10.1002/pld3.316

Qiao, H., & Stepanova, A. N. (2021, October). Editorial overview: Toward deciphering the molecular basis of plant phenotypic plasticity. CURRENT OPINION IN PLANT BIOLOGY, Vol. 63. https://doi.org/10.1016/j.pbi.2021.102107

Zhao, C., Yaschenko, A., Alonso, J. M., & Stepanova, A. N. (2021). Leveraging synthetic biology approaches in plant hormone research. Current Opinion in Plant Biology. https://doi.org/10.1016/j.pbi.2020.101998

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

Stepanova, A. N. (2021, September 30). Plant Biology Research: What Is Next? FRONTIERS IN PLANT SCIENCE, Vol. 12. https://doi.org/10.3389/fpls.2021.749104

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

Fernandez‐Moreno, J. P., & Stepanova, A. N. (2020). Monitoring Ethylene in Plants: Genetically Encoded Reporters and Biosensors. Small Methods. https://doi.org/10.1002/smtd.201900260

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

Zander, M., Willige, B. C., He, Y., Nguyen, T. A., Langford, A. E., Nehring, R., … Ecker, J. R. (2019). Epigenetic silencing of a multifunctional plant stress regulator. ELIFE, 8. https://doi.org/10.7554/eLife.47835

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

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

Mazzoni-Putman, S. M., & Stepanova, A. N. (2018). [Review of A Plant Biologist's Toolbox to Study Translation]. FRONTIERS IN PLANT SCIENCE, 9. https://doi.org/10.3389/fpls.2018.00873

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

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

Ferrando, A., Castellano, M. M., Lisón, P., Leister, D., Stepanova, A. N., & Hanson, J. (2017). Editorial: Relevance of translational regulation on plant growth and environmental responses. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.02170

Merchante, C., & Stepanova, A. N. (2017). The triple response assay and its use to characterize ethylene mutants in Arabidopsis. Ethylene Signaling: Methods and Protocols, 1573, 163–209.

Merchante, C., & Stepanova, A. N. (2017). The triple response assay and its use to characterize ethylene mutants in arabidopsis. In Methods in Molecular Biology (Vol. 1573, pp. 163–209). https://doi.org/10.1007/978-1-4939-6854-1_13

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

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., Merchante, C., STEPANOVA, A. N. N. A., Alonso, J., & Heber, S. (2016). Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana. IEEE Transactions on Nanobioscience, 15(2), 150–159. https://doi.org/10.1109/TNB.2016.2516950

Villarino, G. H., Hu, Q., Manrique, S., Flores-Vergara, M., Sehra, B., Robles, L., … Franks, R. G. (2016). Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain. PLANT PHYSIOLOGY, 171(1), 42–61. https://doi.org/10.1104/pp.15.01845

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

Alonso, J., & STEPANOVA, A. N. N. A. (2015). A recombineering-based gene tagging system for Arabidopsis. Methods in Molecular Biology (Clifton, N.J.), 1227, 233–243. https://doi.org/10.1007/978-1-4939-1652-8_11

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.

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., Merchante, C., STEPANOVA, A. N. N. A., Alonso, J., & Heber, S. (2015). Mining transcript features related to translation in Arabidopsis using LASSO and random forest. 2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2015. 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

Alonso, J. M., & Stepanova, A. N. (2014). Arabidopsis transformation with large bacterial artificial chromosomes. In Methods in Molecular Biology (Vol. 1062, pp. 271–283). https://doi.org/10.1007/978-1-62703-580-4_15

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

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, K., Hu, Q., Stepanova, A. N., Eonso, J. M., & Heber, S. (2013). Deep sequencing of ribosomal footprints for studying genome-wide mRNA translation in plants. 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013. https://doi.org/10.1109/ICCABS.2013.6629221

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

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

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

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

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

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

Stepanova, A. N., & Alonso, J. M. (2006). PCR-based screening for insertional mutants. Methods in Molecular Biology (Clifton, N.J.), 323, 163–172. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-33745265233&partnerID=MN8TOARS

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

Stepanova, A. N., & Alonso, J. M. (2005). Arabidopsis ethylene signaling pathway. Science's STKE : Signal Transduction Knowledge Environment, 2005(276). Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-33644876995&partnerID=MN8TOARS

Stepanova, A. N., & Alonso, J. M. (2005). Ethylene signaling pathway. Science's STKE : Signal Transduction Knowledge Environment, 2005(276). Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-33644877967&partnerID=MN8TOARS

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

Stepanova, A. N., & Alonso, J. M. (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.1399-3054.2005.00447.x

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

Binder, B. M., Mortimore, L. A., Stepanova, A. N., Ecker, JR, & Bleecker, A. B. (2004). Short-term growth responses to ethylene in arabidopsis seedlings are EIN3/EIL1 independent. PLANT PHYSIOLOGY, 136(2), 2921–2927. https://doi.org/10.1104/pp.104.050393

Alonso, J. M., & Stepanova, A. N. (2004). The ethylene signaling pathway. SCIENCE, 306(5701), 1513–1515. https://doi.org/10.1126/science.1104812

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 of the United States of America, 100(5), 2992–2997. https://doi.org/10.1073/pnas.0438070100

Alonso, J. M., Stepanova, A. N., Leisse, T. J., Kim, C. J., Chen, H., Shinn, P., … Ecker, J. R. (2003). Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science, 301(5633), 653–657. https://doi.org/10.1126/science.1086391

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

Alonso, J. M., & Stepanova, A. N. (2003). T-DNA mutagenesis in Arabidopsis. Methods in Molecular Biology (Clifton, N.J.), 236, 177–188. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-1542548233&partnerID=MN8TOARS

Stepanova, A. N., & Ecker, J. R. (2000). Ethylene signaling: From mutants to molecules. Current Opinion in Plant Biology, 3(5), 353–360. https://doi.org/10.1016/S1369-5266(00)00096-0

Solano, R., Stepanova, A., Chao, Q., & Ecker, J. R. (1998). Nuclear events in ethylene signaling: A transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. Genes and Development, 12(23), 3703–3714. https://doi.org/10.1101/gad.12.23.3703