Jose Miguel Alonso Bellver

Recruitment of bifunctional regulator thermospermine to methylated ribosomes directs xylem fate

Ko, D., Ruonala, R., Faille, A., Hellmann, E., Help, H., Liu, H., … Helariutta, Y. (2026, February 12). Science.

EBSn , a Robust Synthetic Reporter for Monitoring Ethylene Responses in Plants

Fernandez‐Moreno, J. P., Fenech, M., Yaschenko, A. E., Zhao, C., Neubauer, M., Davis, H. N., … Stepanova, A. N. (2025, September 21). Plant Biotechnology Journal, Vol. 9.

DASH : a versatile and high‐capacity gene stacking system for plant synthetic biology

Zhao, C., Stepanova, A. N., & Alonso, J. M. (2025, June 10). Plant Biotechnology Journal, Vol. 6.

Arabidopsis lines with modified ascorbate concentrations reveal a link between ascorbate and auxin biosynthesis

Fenech, M., Zulian, V., Moya-Cuevas, J., Arnaud, D., Morilla, I., Smirnoff, N., … Amorim-Silva, V. (2025, May 16). BioRxiv (Cold Spring Harbor Laboratory).

Arabidopsis lines with modified ascorbate concentrations reveal a link between ascorbate and auxin biosynthesis

Fenech, M., Zulian, V., Moya-Cuevas, J., Arnaud, D., Morilla, I., Smirnoff, N., … Amorim-Silva, V. (2025, December 19). PLANT PHYSIOLOGY, Vol. 12.

DASH: A versatile and high-capacity gene stacking system for plant synthetic biology

Zhao, C., Stepanova, A. N., & Alonso, J. M. (2025, March 6). BioRxiv (Cold Spring Harbor Laboratory).

Development of Modular Geminivirus‐Based Vectors for High Cargo Expression and Gene Targeting in Plants

Neubauer, M., Vollen, K., Zhao, C., Ascencio‐Ibáñez, J. T., Hanley‐Bowdoin, L., Stepanova, A. N., & Alonso, J. M. (2025, September 21). Plant Biotechnology Journal, Vol. 9.

Arabidopsis as a model for translational research

The Plant Cell, 2.

Development of modular geminivirus-based vectors for high cargo expression and gene targeting in plants

Sourcing DNA parts for synthetic biology applications in plants

Current Opinion in Biotechnology, 87, 103140.

Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?

Current Opinion in Plant Biology, 68, 102241.

Tandem C2 domains mediate dynamic organelle targeting of a DOCK family guanine nucleotide exchange factor

Mallery, E. L., Yanagisawa, M., Zhang, C., Lee, Y., Robles, L. M., Alonso, J. M., & Szymanski, D. B. (2022, February 23). Journal of Cell Science, Vol. 135.

A G protein-coupled receptor-like module regulates cellulose synthase secretion from the endomembrane system in Arabidopsis

McFarlane, H. E., Mutwil-Anderwald, D., Verbančič, J., Picard, K. L., Gookin, T. E., Froehlich, A., … Persson, S. (2021, April 20). Developmental Cell, Vol. 5.

Auxin Interactions with Other Hormones in Plant Development

Cold Spring Harbor Perspectives in Biology, 13(10), a039990.

Leveraging synthetic biology approaches in plant hormone research

CURRENT OPINION IN PLANT BIOLOGY.

To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses

Plants, 11(1), 33.

Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis

Gomez, M. D., Barro-Trastoy, D., Fuster-Almunia, C., Tornero, P., Alonso, J. M., & Perez-Amador, M. A. (2020, August 21). Journal of Experimental Botany, Vol. 71, pp. 7059–7072.

Regulation of ovule initiation by gibberellins and brassinosteroids in tomato and Arabidopsis: two plant species, two molecular mechanisms

Barro‐Trastoy, D., Carrera, E., Baños, J., Palau‐Rodríguez, J., Ruiz‐Rivero, O., Tornero, P., … Pérez‐Amador, M. A. (2020, January 13). The Plant Journal.

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).

Structure–Function Analysis of Interallelic Complementation in ROOTY Transheterozygotes

Plant Physiology, 183(3), 1110–1125.

An Improved Recombineering Toolset for Plants

The Plant Cell, 32(1), 100–122.

An improved plant toolset for high-throughput recombineering

Brumos, J., Zhao, C., Gong, Y., Soriano, D., Patel, A. P., Perez-Amador, M. A., … Alonso, J. M. (2019, June 3). (Vol. 6). Vol. 6.

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).

From Ethylene-Auxin Interactions to Auxin Biosynthesis and Signal Integration

The Plant Cell, 31(7), 1393–1394.

RGL2 controls flower development, ovule number and fertility in Arabidopsis

Gómez, M. D., Fuster-Almunia, C., Ocaña-Cuesta, J., Alonso, J. M., & Pérez-Amador, M. A. (2019, January 23). Plant Science, Vol. 281, pp. 82–92.

RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data

BMC Genomics, 20(S5).

A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate

Nature Communications, 9(1).

Author Correction: A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate

Nature Communications, 9(1), 1818.

Gibberellins negatively modulate ovule number in plants

Development, 145(13), dev163865.

Local Auxin Biosynthesis Is a Key Regulator of Plant Development

Developmental Cell, 47(3), 306–318.e5.

Microtubule-Dependent Confinement of a Cell Signaling and Actin Polymerization Control Module Regulates Polarized Cell Growth

Current Biology, 28(15), 2459–2466.e4.

Corrigendum: Transcriptomic Analysis in Strawberry Fruits Reveals Active Auxin Biosynthesis and Signaling in the Ripe Receptacle

Estrada-Johnson, E., Csukasi, F., Pizarro, C. M., Vallarino, J. G., Kiryakova, Y., Vioque, A., … Valpuesta, V. (2017, July 24). Frontiers in Plant Science, Vol. 8.

Transcriptomic analysis in strawberry fruits reveals active auxin biosynthesis and signaling in the ripe receptacle

Frontiers in Plant Science, 8.

Translation regulation in plants: an interesting past, an exciting present and a promising future

The Plant Journal, 90(4), 628–653.

Translation regulation of uORFs-containing genes in Arabidopsis

50 years of Arabidopsis research: Highlights and future directions

[Review of ]. New Phytologist, 209(3), 921–944.

A Ribosome Footprinting Protocol for Plants

BIO-PROTOCOL, 6(21).

Auxin catabolism unplugged: Role of IAA oxidation in auxin homeostasis

Proceedings of the National Academy of Sciences, 113(39), 10742–10744.

Cutting Out the Middle Man in Light-Hormone Interactions

Developmental Cell, 39(5), 524–526.

Genome-wide search for translated upstream open reading frames in Arabidopsis thaliana

IEEE Transactions on Nanobioscience, 15(2), 150–159.

Hormone-Mediated Gene-Specific Translation Regulation

http://hdl.handle.net/10630/11885

A Recombineering-based gene tagging system for Arabidopsis

Bacterial Artificial Chromosomes, 2nd Edition, 1227, 233–243.

A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana

In Bioinformatics Research and Applications (Vol. 9096, pp. 138–149).

A stacking-based approach to identify translated upstream open reading frames in Arabidopsis thaliana

Bioinformatics research and applications (isbra 2015), 9096, 138–149.

Auxin Influx Carriers Control Vascular Patterning and Xylem Differentiation in Arabidopsis thaliana

Fàbregas, N., Formosa-Jordan, P., Confraria, A., Siligato, R., Alonso, J. M., Swarup, R., … Ibañes, M. (2015, April 29). PLoS Genetics, Vol. 11.

Bird and Scarecrow proteins organize tissue formation in Arabidopsis roots

Science, 350(6259), 426–430.

Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2

Cell, 163(3), 684–697.

Mining transcript features related to translation in Arabidopsis using LASSO and random forest

Hu, N. Q., Merchante, C., Stepanova, A. N., Alonso, J. M., & Heber, S. (2015, October 1). International Conference on Computational Advances in Bio and Medical.

Plant functional genomics methods and protocols second edition preface

Plant Functional Genomics: Methods and Protocols, 2nd Edition, 1284, V-.

Plant functional genomics: Methods and protocols

In J. M. Alonso & A. N. Stepanova (Eds.), Methods in molecular biology (2nd ed., pp. 1–526).

REGULATOR OF BULB BIOGENESIS1 (RBB1) Is Involved in Vacuole Bulb Formation in Arabidopsis

Han, S. W., Alonso, J. M., & Rojas-Pierce, M. (2015, April 27). (D. Bassham, Ed.). PLoS ONE, Vol. 10, p. e0125621.

Arabidopsis Transformation with Large Bacterial Artificial Chromosomes

In Arabidopsis Protocols (pp. 271–283).

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.

Systems analysis of auxin transport in the arabidopsis root apex

Plant Cell, 26(3), 862–875.

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.

Arabidopsis SABRE and CLASP interact to stabilize cell division plane orientation and planar polarity

Nature Communications, 4(1).

Ethylene signaling: simple ligand, complex regulation

Current Opinion in Plant Biology, 16(5), 554–560.

Functional Characterization of Type-B Response Regulators in the Arabidopsis Cytokinin Response    

Plant Physiology, 162(1), 212–224.

Genetic aspects of auxin biosynthesis and its regulation

Physiologia Plantarum, 151(1), 3–12.

Local Auxin Sources Orient the Apical-Basal Axis in Arabidopsis Embryos

Current Biology, 23(24), 2506–2512.

Molecular Mechanisms of Ethylene–Auxin Interaction

Molecular Plant, 6(6), 1734–1737.

Molecular mechanisms of ethylene–auxin interactions

Molecular Plant, sst113.

AUX/LAX Genes Encode a Family of Auxin Influx Transporters That Perform Distinct Functions during Arabidopsis Development

Péret, B., Swarup, K., Ferguson, A., Seth, M., Yang, Y., Dhondt, S., … Swarup, R. (2012, July 1). The Plant Cell, Vol. 24, pp. 2874–2885.

AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during arabidopsis development

Plant Cell, 24(7), 2874–2885.

Kinetic analysis of Arabidopsis glucosyltransferase UGT74B1 illustrates a general mechanism by which enzymes can escape product inhibition

Biochemical Journal, 450(1), 37–46.

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

A Small-Molecule Screen Identifiesl-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.

A recombineering‐based gene tagging system for Arabidopsis

The Plant Journal, 66(4), 712–723.

A recombineering‐based gene tagging system for Arabidopsis

The Plant Journal, 66(4), 712–723.

Bypassing Transcription: A Shortcut in Cytokinin-Auxin Interactions

Developmental Cell, 21(4), 608–610.

The Arabidopsis YUCCA1 Flavin Monooxygenase Functions in the Indole-3-Pyruvic Acid Branch of Auxin Biosynthesis

The Plant Cell, 23(11), 3961–3973.

A Combinatorial Interplay Among the 1-Aminocyclopropane-1-Carboxylate Isoforms Regulates Ethylene Biosynthesis inArabidopsis thaliana

Tsuchisaka, A., Yu, G., Jin, H., Alonso, J. M., Ecker, J. R., Zhang, X., … Theologis, A. (2009, September 15). Genetics, Vol. 183, pp. 979–1003.

Ethylene signaling and response: where different regulatory modules meet

Current Opinion in Plant Biology, 12(5), 548–555.

Local auxin biosynthesis modulates gradient-directed planar polarity in Arabidopsis

Nature Cell Biology, 11(6), 731–738.

Potential Sites of Bioactive Gibberellin Production during Reproductive Growth inArabidopsis 

Hu, J., Mitchum, M. G., Barnaby, N., Ayele, B. T., Ogawa, M., Nam, E., … Sun, T.-ping. (2008, February 1). The Plant Cell, Vol. 20, pp. 320–336.