Ross Sozzani

Madison, I., Tahir, M., Broeck, L. V., Phan, L., Horn, T., & Sozzani, R. (2024, February 1). Cell-material interactions in 3D bioprinted plant cells. https://doi.org/10.1101/2024.01.30.578043

Haverroth, E., Gobble, M., Bradley, L., Harris-Gilliam, K., Fischer, A., Williams, C., … Sozzani, R. (2024, January 29). The Black American experience: Answering the global challenge of broadening participation in STEM/agriculture. PLANT CELL, Vol. 1. https://doi.org/10.1093/plcell/koae002

Van den Broeck, L., Bhosale, D. K., Song, K., Fonseca de Lima, C. F., Ashley, M., Zhu, T., … Sozzani, R. (2023). Functional annotation of proteins for signaling network inference in non-model species. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-40365-z

Bennett, M. J., Brady, S. M., Dinneny, J. R., Helariutta, Y., & Sozzani, R. (2023, November 20). Obituary Philip N. Benfey (1953-2023). DEVELOPMENTAL CELL, Vol. 58, pp. 2413–2415. https://doi.org/10.1016/j.devcel.2023.10.013

Madison, I., Gillan, L., Peace, J., Gabrieli, F., Broeck, L., Jones, J. L., & Sozzani, R. (2023, August 23). Phosphate starvation: response mechanisms and solutions (D. Ort, Ed.). JOURNAL OF EXPERIMENTAL BOTANY, Vol. 8. https://doi.org/10.1093/jxb/erad326

Mahatma, S., Broeck, L. V., Morffy, N., Staller, M. V., Strader, L. C., & Sozzani, R. (2023, March 22). Prediction and functional characterization of transcriptional activation domains. https://doi.org/10.1109/CISS56502.2023.10089768

Gaudinier, A., Broeck, L. V., Moreno-Risueño, M., Rodriguez-Medina, J., Sozzani, R., & Brady, S. M. (2023, December 6). Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation. https://doi.org/10.1101/2023.12.05.570292

Beretta, V. M., Franchini, E., Din, I. U., Lacchini, E., Broeck, L., Sozzani, R., … Kater, M. M. (2023, April 21). The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice. PLANT JOURNAL, Vol. 4. https://doi.org/10.1111/tpj.16229

Ortiz, A. C., De Smet, I., Sozzani, R., & Locke, A. M. (2022). Field-grown soybean shows genotypic variation in physiological and seed composition responses to heat stress during seed development. Environmental and Experimental Botany, 195, 104768. https://doi.org/10.1016/j.envexpbot.2021.104768

Thomas, H., Broeck, L., Spurney, R., Sozzani, R., & Frank, M. (2022). Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation. PLANT CELL, 34(1), 535–556. https://doi.org/10.1093/plcell/koab246

Muhammad, D. S., Clark, N. M., Haque, S., Williams, C. M., Sozzani, R., & Long, T. A. (2022, August 3). POPEYE intercellular localization mediates cell-specific iron deficiency responses. PLANT PHYSIOLOGY, Vol. 8. https://doi.org/10.1093/plphys/kiac357

Adhikari, T. B., Aryal, R., Redpath, L. E., Broeck, L., Ashrafi, H., Philbrick, A. N., … Louws, F. J. (2022). RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry. FRONTIERS IN GENETICS, 12. https://doi.org/10.3389/fgene.2021.805771

Broeck, L. V., Spurney, R. J., Fisher, A. P., Schwartz, M., Clark, N. M., Nguyen, T. T., … Sozzani, R. (2021). A hybrid model connecting regulatory interactions with stem cell divisions in the root. Quantitative Plant Biology, 2. https://doi.org/10.1017/qpb.2021.1

Roszak, P., Heo, J.-O., Blob, B., Toyokura, K., Sugiyama, Y., Balaguer, M. A. de L., … Helariutta, Y. (2021). Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization. SCIENCE, 374(6575), 1577-+. https://doi.org/10.1126/science.aba5531

Schwartz, M. F., Peters, R., Hunt, A. M., Abdul-Matin, A.-K., Broeck, L., & Sozzani, R. (2021). [Review of Divide and Conquer: The Initiation and Proliferation of Meristems]. CRITICAL REVIEWS IN PLANT SCIENCES, 40(2), 147–156. https://doi.org/10.1080/07352689.2021.1915228

Orozco-Navarrete, B., Song, J., Casanal, A., Sozzani, R., Flors, V., Sanchez-Sevilla, J. F., … Valpuesta, V. (2021). Down-regulation of Fra a 1.02 in strawberry fruits causes transcriptomic and metabolic changes compatible with an altered defense response. HORTICULTURE RESEARCH, 8(1). https://doi.org/10.1038/s41438-021-00492-4

Thomas, H., Broeck, L. V., Spurney, R., Sozzani, R., & Frank, M. (2021, February 27). Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation (Vol. 2). Vol. 2. https://doi.org/10.1101/2021.02.26.433082

Clark, N. M., Nolan, T. M., Wang, P., Song, G., Montes, C., Valentine, C. T., … Walley, J. W. (2021). Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis. NATURE COMMUNICATIONS, 12(1). https://doi.org/10.1038/s41467-021-26165-3

Betegon-Putze, I., Mercadal, J., Bosch, N., Planas-Riverola, A., Marques-Bueno, M., Vilarrasa-Blasi, J., … Cano-Delgado, A. I. (2021). Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots. MOLECULAR SYSTEMS BIOLOGY, 17(6). https://doi.org/10.15252/msb.20209864

Spurney, R., Schwartz, M., Gobble, M., Sozzani, R., & Broeck, L. (2021). Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification. MODELING TRANSCRIPTIONAL REGULATION, Vol. 2328, pp. 47–65. https://doi.org/10.1007/978-1-0716-1534-8_4

Crook, A. D., Willoughby, A. C., Hazak, O., Okuda, S., VanDerMolen, K. R., Soyars, C. L., … Nimchuk, Z. L. (2020). BAM1/2 receptor kinase signaling drives CLE peptide-mediated formative cell divisions in Arabidopsis roots. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 117(51), 32750–32756. https://doi.org/10.1073/pnas.2018565117

Buckner, E., Madison, I., Melvin, C., Long, T., Sozzani, R., & Williams, C. (2020). BioVision Tracker: A semi-automated image analysis software for spatiotemporal gene expression tracking in Arabidopsis thaliana. In Methods in Cell Biology (Vol. 160, pp. 419–436). https://doi.org/10.1016/bs.mcb.2020.04.017

Van Norman, J. M., Strader, L. C., & Sozzani, R. (2020, October). Editorial overview: Directionality and precision - how signaling and gene regulation drive plant development and growth. CURRENT OPINION IN PLANT BIOLOGY, Vol. 57, pp. A1–A3. https://doi.org/10.1016/j.pbi.2020.11.001

Broeck, L. V., Spurney, R. J., Fisher, A. P., Schwartz, M., Clark, N. M., Nguyen, T. T., … Sozzani, R. (2020, December 1). Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions. https://doi.org/10.1101/2020.11.30.404426

Van den Broeck, L., Gordon, M., Inzé, D., Williams, C., & Sozzani, R. (2020). Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling. Frontiers in Genetics, 11. https://doi.org/10.3389/fgene.2020.00457

Madison, I., Melvin, C., Buckner, E., Williams, C., Sozzani, R., & Long, T. (2020). MAGIC: Live imaging of cellular division in plant seedlings using lightsheet microscopy. In Methods in Cell Biology (Vol. 160, pp. 405–418). https://doi.org/10.1016/bs.mcb.2020.04.004

Clark, N. M., Van den Broeck, L., Guichard, M., Stager, A., Tanner, H. G., Blilou, I., … Sozzani, R. (2020). Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big. Annual Review of Plant Biology, 71(1), 789–816. https://doi.org/10.1146/annurev-arplant-050718-100038

Clark, N. M., Fisher, A. P., Berckmans, B., Van den Broeck, L., Nelson, E. C., Nguyen, T. T., … Sozzani, R. (2020). Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division. Proceedings of the National Academy of Sciences, 117(26), 15332–15342. https://doi.org/10.1073/pnas.2002166117

Spurney, R. J., Broeck, L., Clark, N. M., Fisher, A. P., Balaguer, M. A. de L., & Sozzani, R. (2020). tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks. PLANT JOURNAL, 101(3), 716–730. https://doi.org/10.1111/tpj.14558

Buckner, E., Madison, I., Chou, H., Matthiadis, A., Melvin, C. E., Sozzani, R., … Long, T. A. (2019). Automated Imaging, Tracking, and Analytics Pipeline for Differentiating Environmental Effects on Root Meristematic Cell Division. Frontiers in Plant Science, 10. https://doi.org/10.3389/fpls.2019.01487

Vallarino, J. G., Merchante, C., Sánchez‐Sevilla, J. F., Luis Balaguer, M. A., Pott, D. M., Ariza, M. T., … Osorio, S. (2019). Characterizing the involvement of
            FaMADS9
            in the regulation of strawberry fruit receptacle development. Plant Biotechnology Journal, 18(4), 929–943. https://doi.org/10.1111/pbi.13257

Haque, S., Ahmad, J. S., Clark, N. M., Williams, C. M., & Sozzani, R. (2019). Computational prediction of gene regulatory networks in plant growth and development. Current Opinion in Plant Biology, 47, 96–105. https://doi.org/10.1016/j.pbi.2018.10.005

Smet, W., Sevilem, I., Luis Balaguer, M. A., Wybouw, B., Mor, E., Miyashima, S., … De Rybel, B. (2019). DOF2.1 Controls Cytokinin-Dependent Vascular Cell Proliferation Downstream of TMO5/LHW. CURRENT BIOLOGY, 29(3), 520-+. https://doi.org/10.1016/j.cub.2018.12.041

Miyashima, S., Roszak, P., Sevilem, I., Toyokura, K., Blob, B., Heo, J.-ok, … Helariutta, Y. (2019). Mobile PEAR transcription factors integrate hormone and miRNA cues to prime cambial growth. Nature, 565(7740), 490–494. https://doi.org/10.1038/s41586-018-0839-y

Powers, S. K., Holehouse, A. S., Korasick, D. A., Schreiber, K. H., Clark, N. M., Jing, H., … Strader, L. C. (2019). Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana. MOLECULAR CELL, 76(1), 177-+. https://doi.org/10.1016/j.molcel.2019.06.044

Clark, N. M., Buckner, E., Fisher, A. P., Nelson, E. C., Nguyen, T. T., Simmons, A. R., … Sozzani, R. (2019). Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks. NATURE COMMUNICATIONS, 10. https://doi.org/10.1038/s41467-019-13132-2

Di Mambro, R., Svolacchia, N., Dello Ioio, R., Pierdonati, E., Salvi, E., Pedrazzini, E., … Sabatini, S. (2019). The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size. CURRENT BIOLOGY, 29(7), 1199-+. https://doi.org/10.1016/j.cub.2019.02.022

O'Lexy, R., Kasai, K., Clark, N., Fujiwara, T., Sozzani, R., & Gallagher, K. L. (2018). Exposure to heavy metal stress triggers changes in plasmodesmatal permeability via deposition and breakdown of callose. JOURNAL OF EXPERIMENTAL BOTANY, 69(15), 3715–3728. https://doi.org/10.1093/jxb/ery171

Shibata, M., Breuer, C., Kawamura, A., Clark, N. M., Rymen, B., Braidwood, L., … Sugimoto, K. (2018). GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis. DEVELOPMENT, 145(3). https://doi.org/10.1242/dev.159707

Clark, N. M., Fisher, A. P., & Sozzani, R. (2018). Identifying Differentially Expressed Genes Using Fluorescence-Activated Cell Sorting (FACS) and RNA Sequencing from Low Input Samples. In L. von Stechow & A. Santos Delgado (Eds.), Computational Cell Biology (pp. 139–151). https://doi.org/10.1007/978-1-4939-8618-7_6

Buckner, E., Ottley, C., Williams, C., Luis Balaguer, A. de, Melvin, C. E., & Sozzani, R. (2018). Tracking Gene Expression via Light Sheet Microscopy and Computer Vision in Living Organisms. 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 818–821. https://doi.org/10.1109/EMBC.2018.8512416

Di Mambro, R., De Ruvo, M., Pacifici, E., Salvi, E., Sozzani, R., Benfey, P. N., … Sabatini, S. (2017). Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(36), E7641–E7649. https://doi.org/10.1073/pnas.1705833114

Liao, K.-L., Melvin, C. E., Sozzani, R., Jones, R. D., Elston, T. C., & Jones, A. M. (2017). Dose-Duration Reciprocity for G protein activation: Modulation of kinase to substrate ratio alters cell signaling. PLOS ONE, 12(12). https://doi.org/10.1371/journal.pone.0190000

Wendrich, J. R., Moller, B. K., Li, S., Saiga, S., Sozzani, R., Benfey, P. N., … Weijers, D. (2017). Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(42), E8922–E8929. https://doi.org/10.1073/pnas.1707400114

Coneva, V., Frank, M. H., Balaguer, M. A. de L., Li, M., Sozzani, R., & Chitwood, D. H. (2017). Genetic Architecture and Molecular Networks Underlying Leaf Thickness in Desert-Adapted Tomato Solanum pennellii. PLANT PHYSIOLOGY, 175(1), 376–391. https://doi.org/10.1104/pp.17.00790

de Luis Balaguer, M. A., & Sozzani, R. (2017). Inferring Gene Regulatory Networks in the Arabidopsis Root Using a Dynamic Bayesian Network Approach. In K. Kaufmann & B. Mueller-Roeber (Eds.), Plant Gene Regulatory Networks (pp. 331–348). https://doi.org/10.1007/978-1-4939-7125-1_21

Clark, N. M., & Sozzani, R. (2017). Measuring Protein Movement, Oligomerization State, and Protein–Protein Interaction in Arabidopsis Roots Using Scanning Fluorescence Correlation Spectroscopy (Scanning FCS). In W. Busch (Ed.), Plant Genomics (pp. 251–266). https://doi.org/10.1007/978-1-4939-7003-2_16

Balaguer, M. A. D., Fisher, A. P., Clark, N. M., Fernandez-Espinosa, M. G., Moller, B. K., Weijers, D., … al. (2017). Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(36), E7632–E7640. https://doi.org/10.1073/pnas.1707566114

Fisher, A. P., & Sozzani, R. (2016). Gene and networks regulating the root stem cell niche of Arabidopsis. Curr Opin Plant Biol, 29, 38–43. https://doi.org/10.1016/j.pbi.2015.11.002

Slattery, R. A., Grennan, A. K., Sivaguru, M., Sozzani, R., & Ort, D. R. (2016). Light sheet microscopy reveals more gradual light attenuation in light-green versus dark-green soybean leaves. JOURNAL OF EXPERIMENTAL BOTANY, 67(15), 4697–4709. https://doi.org/10.1093/jxb/erw246

de Luis Balaguer, M. A., Ramos-Pezzotti, M., Rahhal, M. B., Melvin, C. E., Johannes, E., Horn, T. J., & Sozzani, R. (2016). Multi-sample Arabidopsis Growth and Imaging Chamber (MAGIC) for long term imaging in the ZEISS Lightsheet Z.1. Developmental Biology, 419(1), 19–25. https://doi.org/10.1016/j.ydbio.2016.05.029

Clark, N. M., Hinde, E., Winter, C. M., Fisher, A. P., Crosti, G., Blilou, I., … Sozzani, R. (2016). Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy. Elife, 5.

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

Sozzani, R., Busch, W., Spalding, E. P., & Benfey, P. N. (2014). [Review of Advanced imaging techniques for the study of plant growth and development]. TRENDS IN PLANT SCIENCE, 19(5), 304–310. https://doi.org/10.1016/j.tplants.2013.12.003

Clark, N. M., Balaguer, M. A. D., & Sozzani, R. (2014). [Review of Experimental data and computational modeling link auxin gradient and development in the Arabidopsis root]. Frontiers in Plant Science, 5.

Gallagher, K. L., Sozzani, R., & Lee, C.-M. (2014). Intercellular Protein Movement: Deciphering the Language of Development. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 30, Vol. 30, pp. 207–233. https://doi.org/10.1146/annurev-cellbio-100913-012915

Kajala, K., Ramakrishna, P., Fisher, A., Bergmann, D. C., De Smet, I., Sozzani, R., … Brady, S. M. (2014). [Review of Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants]. ANNALS OF BOTANY, 113(7), 1083–1105. https://doi.org/10.1093/aob/mcu065

Sozzani, R., & Iyer-Pascuzzi, A. (2014). [Review of Postembryonic control of root meristem growth and development]. CURRENT OPINION IN PLANT BIOLOGY, 17, 7–12. https://doi.org/10.1016/j.pbi.2013.10.005

Moubayidin, L., Di Mambro, R., Sozzani, R., Pacifici, E., Salvi, E., Terpstra, I., … Sabatini, S. (2013). Spatial Coordination between Stem Cell Activity and Cell Differentiation in the Root Meristem. Developmental Cell, 26(4), 405–415. https://doi.org/10.1016/j.devcel.2013.06.025

Cruz-Ramírez, A., Díaz-Triviño, S., Blilou, I., Grieneisen, V. A., Sozzani, R., Zamioudis, C., … Scheres, B. (2012). A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell, 150(5), 1002–1015. https://doi.org/10.1016/j.cell.2012.07.017

Liberman, L. M., Sozzani, R., & Benfey, P. N. (2012). Integrative systems biology: an attempt to describe a simple weed. Current Opinion in Plant Biology, 15(2), 162–167. https://doi.org/10.1016/j.pbi.2012.01.004

Engstrom, E. M., Andersen, C. M., Gumulak-Smith, J., Hu, J., Orlova, E., Sozzani, R., & Bowman, J. L. (2011). Arabidopsis homologs of the petunia hairy meristem gene are required for maintenance of shoot and root indeterminacy. Plant Physiology, 155(2), 735–750. https://doi.org/10.1104/pp.110.168757

Sozzani, R., & Benfey, P. N. (2011). High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype. Genome Biology, 12(3), 219. https://doi.org/10.1186/gb-2011-12-3-219

Sozzani, R., Cui, H., Moreno-Risueno, M. A., Busch, W., Van Norman, J. M., Vernoux, T., … Benfey, P. N. (2010). Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature, 466(7302), 128–132. https://doi.org/10.1038/nature09143

Sozzani, R., Maggio, C., Giordo, R., Umana, E., Ascencio-Ibañez, J. T., Hanley-Bowdoin, L., … Albani, D. (2010). The E2FD/DEL2 factor is a component of a regulatory network controlling cell proliferation and development in Arabidopsis. Plant Molecular Biology, 72(4-5), 381–395. https://doi.org/10.1007/s11103-009-9577-8

Sozzani, R., Cui, H., Moreno-Risueno, M. A., Busch, W., Van Norman, J. M., Vernoux, T., … Benfey, P. N. (2010). The SHR/SCR pathway directly activates genes involved in asymmetric cell division in the Arabidopsis root. Nature, 466(7302), 128–132.

Benfey, P. N., Cui, H., Twigg, R., Long, T., Iyer-Pascuzzi, A., Tsukagoshi, H., … Moreno-Risueno, M. (2009). Development rooted in interwoven networks. Developmental Biology, 331(2), 386. https://doi.org/10.1016/j.ydbio.2009.05.012

Ni, D. A., Sozzani, R., Blanchet, S., Domenichini, S., Reuzeau, C., Cella, R., … Raynaud, C. (2009). The Arabidopsis MCM2 gene is essential to embryo development and its over-expression alters root meristem function. The New Phytologist, 184(2), 311–322. https://doi.org/10.1111/j.1469-8137.2009.02961.x

Ascencio-Ibáñez, J. T., Sozzani, R., Lee, T.-J., Chu, T.-M., Wolfinger, R. D., Cella, R., & Hanley-Bowdoin, L. (2008). Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiology, 148(1), 436–454. https://doi.org/10.1104/pp.108.121038

Sozzani, R., Maggio, C., Varotto, S., Canova, S., Bergounioux, C., Albani, D., & Cella, R. (2006). Interplay between Arabidopsis Activating Factors E2Fb and E2Fa in Cell Cycle Progression and Development. Plant Physiology, 140(4), 1355–1366. https://doi.org/10.1104/pp.106.077990

Raynaud, C., Sozzani, R., Glab, N., Domenichini, S., Perennes, C., Cella, R., … Bergounioux, C. (2006). Two cell-cycle regulated SET-domain proteins interact with proliferating cell nuclear antigen (PCNA) in Arabidopsis. The Plant Journal: For Cell and Molecular Biology, 47(3), 395–407. https://doi.org/10.1111/j.1365-313X.2006.02799.x