Jose Miguel Alonso Bellver

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

[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 68.

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

JOURNAL OF CELL SCIENCE, 135(7).

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

PLANTS-BASEL, 11(1).

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

DEVELOPMENTAL CELL, 56(10), 1484-+.

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

[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 60.

An Improved Recombineering Toolset for Plants

The Plant Cell.

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).

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

JOURNAL OF EXPERIMENTAL BOTANY, 71(22), 7059–7072.

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

The Plant Journal, 102(5), 1026–1041.

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 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.

From Ethylene-Auxin Interactions to Auxin Biosynthesis and Signal Integration

Stepanova, A. N., & Alonso, J. M. (2019, July). PLANT CELL, Vol. 31, pp. 1393–1394.

RGL2 controls flower development, ovule number and fertility in Arabidopsis

PLANT SCIENCE, 281, 82–92.

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

Perkins, P., Mazzoni-Putman, S., Stepanova, A., Alonso, J., & Heber, S. (2019, June 6). BMC GENOMICS, Vol. 20.

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-+.

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

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

Transcriptomic Analysis in Strawberry Fruits Reveals Active Auxin Biosynthesis and Signaling in the Ripe Receptacle (vol 8, pg 889, 2017)

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

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

Stepanova, A. N., & Alonso, J. M. (2016, September 27). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol. 113, pp. 10742–10744.

Cutting Out the Middle Man in Light-Hormone Interactions

Stepanova, A. N., & Alonso, J. M. (2016, December 5). DEVELOPMENTAL CELL, Vol. 39, pp. 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

PLOS GENETICS, 11(4).

Bird and Scarecrow proteins organize tissue formation in Arabidopsis roots

Science, 350(6259), 426–430.

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.

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

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.), Plant Functional Genomics: Methods and Protocols: Second Edition (2nd ed., pp. 1–526).

Regulator of bulb biogenesis1 (RBB1) is involved in vacuole bulb formation in arabidopsis

PLoS One, 10(4), e0125621.

Arabidopsis Transformation with Large Bacterial Artificial Chromosomes

In Arabidopsis Protocols (pp. 271–283).

Genetic aspects of auxin biosynthesis and its regulation

PHYSIOLOGIA PLANTARUM, 151(1), 3–12.

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.

Ethylene signaling: simple ligand, complex regulation

[Review of ]. 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.

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

BIOCHEMICAL JOURNAL, 450(1), 37–46.

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

CURRENT BIOLOGY, 23(24), 2506–2512.

Molecular Mechanisms of EthyleneAuxin 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

The Plant Cell Online, 24(7), 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.

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.

A recombineering-based gene tagging system for Arabidopsis

PLANT JOURNAL, 66(4), 712–723.

Bypassing Transcription: A Shortcut in Cytokinin-Auxin Interactions

Stepanova, A. N., & Alonso, J. M. (2011, October 18). DEVELOPMENTAL CELL, Vol. 21, pp. 608–610.

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

PLANT CELL, 23(11), 3961–3973.

A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana

Genetics, 183(3), 979–1003.

Ethylene signaling and response: where different regulatory modules meet

[Review of ]. 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–U70.

Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis

The Plant Cell Online, 20(2), 320–336.

TAA1-Mediated Auxin Biosynthesis Is Essential for Hormone Crosstalk and Plant Development

Cell, 133(1), 177–191.

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.

A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis

PLANT CELL, 19(8), 2403–2416.

An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome

NATURE PROTOCOLS, 2(11), 2910–2917.

Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the< i> Arabidopsis Transcriptome

Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the< i> Arabidopsis Transcriptome. Cell, 131(7), 1340–1353.

Multilevel interactions between ethylene and auxin in Arabidopsis roots

PLANT CELL, 19(7), 2169–2185.

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.

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.

Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1

SCIENCE, 314(5803), 1295–1298.

Molecular mechanisms of ethylene signaling in Arabidopsis

Molecular BioSystems, 2(3-4), 165.

Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis

Nature Reviews Genetics, 7(7), 524–536.

PCR-based screening for insertional mutants

In Arabidopsis Protocols (pp. 163–172).

PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism

Proceedings of the National Academy of Sciences, 103(26), 10134–10139.

RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis

Journal of Experimental Botany, 57(11), 2697–2708.

The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling

The Plant Cell Online, 18(11), 3073–3087.

" Flagellin is not a major defense elicitor in Ralstonia solanacearum cells (vol 17, pg 696, 2005)

MOLECULAR PLANT-MICROBE INTERACTIONS, 18(9), 1024.

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.

An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance

PLANT JOURNAL, 41(2), 304–318.

Arabidopsis ethylene signaling pathway

Science Signaling, 2005(276), cm4.

Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation

Development, 132(18), 4107–4118.

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.

Ethylene signalling and response pathway: A unique signalling cascade with a multitude of inputs and outputs

Physiologia Plantarum, 123(2), 195–206.

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.

Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana

The Plant Cell Online, 17(12), 3282–3300.

Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis

The Plant Cell Online, 17(11), 3007–3018.

NPH4/ARF7 and ARF19 promote leaf expansion and auxin‐induced lateral root formation

The Plant Journal, 43(1), 118–130.

Phytochrome-Specific Type 5 Phosphatase Controls Light Signal Flux by Enhancing Phytochrome Stability and Affinity for a Signal Transducer

Cell, 120(3), 395–406.

Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer

Cell, 120(3), 395–406.

A Homolog of Prokaryotic Thiol Disulfide Transporter CcdA Is Required for the Assembly of the Cytochrome b6f Complex in Arabidopsis Chloroplasts

Journal of Biological Chemistry, 279(31), 32474–32482.

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.

Convergence of Signaling Pathways in the Control of Differential Cell Growth in< i> Arabidopsis

Convergence of Signaling Pathways in the Control of Differential Cell Growth in< i> Arabidopsis. Developmental Cell, 7(2), 193–204.

Convergence of signaling of differential cell growth pathways in the control in Arabidopsis

Developmental Cell, 7(2), 193–204.

DELLA proteins and gibberellin-regulated seed germination and floral development in Arabidopsis

Plant Physiology, 135(2), 1008–1019.

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.

GCR1 can act independently of heterotrimeric G-protein in response to brassinosteroids and gibberellins in Arabidopsis seed germination

Plant Physiology, 135(2), 907–915.

Regulation of flowering time in Arabidopsis by K homology domain proteins

Proceedings of the National Academy of Sciences, 101(34), 12759–12764.

The canonical ethylene signaling pathway

Science Signaling, 2004(221), cm1.

The ethylene signaling pathway

SCIENCE, 306(5701), 1513–1515.

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.

Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling

The Plant Cell Online, 16(3), 658–671.

< i> Arabidopsis RIN4 Is a Target of the Type III Virulence Effector AvrRpt2 and Modulates RPS2-Mediated Resistance

< i> Arabidopsis RIN4 Is a Target of the Type III Virulence Effector AvrRpt2 and Modulates RPS2-Mediated Resistance. Cell, 112(3), 379–389.

A growth regulatory loop that provides homeostasis to phytochrome A signaling

The Plant Cell Online, 15(12), 2966–2978.

Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX

Nature, 421(6918), 79–83.

Enhanced fitness conferred by naturally occurring variation in the circadian clock

Science, 302(5647), 1049–1053.

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.

GUN4, a regulator of chlorophyll synthesis and intracellular signaling

Science, 299(5608), 902–906.

Genome-wide insertional mutagenesis of Arabidopsis thaliana

Science, 301(5633), 653–657.

Genome-wide insertional mutagenesis of Arabidopsis thaliana (vol 301, pg 653, 2003)

Science, 301(5641), 1849.

Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways

The Plant Cell Online, 15(9), 1962–1980.

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.

T-DNA mutagenesis in Arabidopsis

In Plant Functional Genomics (pp. 177–187).

The Balance between phytochrome kinase substrate1 and PKS2 Provides Homeostasis for Phytochrome A Signaling in Arabidopsis

The Plant Cell Online.

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.

A role for peroxisomes in photomorphogenesis and development of Arabidopsis

Science, 297(5580), 405–409.

De-Etiolated 1 and Damaged DNA Binding Protein 1 Interact to Regulate< i> Arabidopsis Photomorphogenesis

De-Etiolated 1 and Damaged DNA Binding Protein 1 Interact to Regulate< i> Arabidopsis Photomorphogenesis. Current Biology, 12(17), 1462–1472.

NPSN11 is a cell plate-associated SNARE protein that interacts with the syntaxin KNOLLE

Plant Physiology, 129(2), 530–539.

Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth

Genetics, 162(3), 1445–1456.

Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3

Genes & Development, 16(23), 3100–3112.

An Arabidopsis circadian clock component interacts with both CRY1 and phyB

Nature, 410(6827), 487–490.

Phototropin-related NPL1 controls chloroplast relocation induced by blue light

Nature, 410(6831), 952–954.

The ethylene pathway: a paradigm for plant hormone signaling and interaction

Science Signaling, 2001(70), re1.

Ethylene captures a metal! Metal ions are involved in ethylene perception and signal transduction

Plant and Cell Physiology, 41(5), 548–555.

Involvement of NRAMP1 from Arabidopsis thaliana in iron transport

Biochem. J, 347, 749–755.

Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana

Nature, 408(6814), 816–820.

EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis

Science, 284(5423), 2148–2152.

Ethylene Perception and Response in Citrus Fruit

In Biology and Biotechnology of the Plant Hormone Ethylene II (pp. 137–143).

RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson Disease–Related Copper Transporter, Is Required for Ethylene Signaling in< i> Arabidopsis

RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson Disease–Related Copper Transporter, Is Required for Ethylene Signaling in< i> Arabidopsis. Cell, 97(3), 383–393.

A non-photosynthetic ferredoxin gene is induced by ethylene in Citrus organs

Plant Molecular Biology, 29(6), 1211–1221.

A putative vacuolar processing protease is regulated by ethylene and also during fruit ripening in Citrus fruit

Plant Physiology, 109(2), 541–547.

Evidence for the involvement of ethylene in the expression of specific RNAs during maturation of the orange, a non-climacteric fruit

Plant Molecular Biology, 29(2), 385–390.

Two dimensional gel electrophoresis patterns of total, in vivo labelled and in vitro translated polypeptides from orange flavedo during maturation and following ethylene treatment

Physiologia Plantarum, 85(2), 147–156.

Deep sequencing of ribosomal footprints for studying genome-wide mRNA translation in plants

Merchante, K., Hu, Q., Stepanova, A. N., Alonso, J. M., & Heber, S.