Publications from NSF Plasticity Project Grants

Manzano C, Morimoto KW, Shaar-Moshe L, Mason GA, Cantó-Pastor A, Gouran M, De Bellis D, Ursache R, Kajala K, Sinha N, Bailey-Serres J, Geldner N, delPozo JC, Brady SM. (2024). Regulation and function of a polarly localized lignin barrier in the exodermis.. Biorxiv. doi:https://doi.org/10.1101/2022.10.20.51311 Accepted by Nature Plants. 

C Bian, GS Demirer, MT Oz, Y Cai, SS Witham, GA Mason, R Shen, A Gaudinier, SM Brady, NJ Patron (2023). Conservation and divergence of regulatoryarchitecture in nitrate-responsive plant gene circuits. bioRxiv 2023.07.17.549299

Wei K, Sharifova S, Zhao X, Sinha N, Nakayama H, Tellier A, Silva-Arias GA. (2024). Evolution of gene networks underlying adaptation to drought stress in the wild tomato Solanum chilense. Molecular Ecology, 

Kawa D, Thiombiano B, Shimels MZ, Taylor T, Walmsley A, Vahldick HE, Rybka D, Leite MFA, Musa Z, Bucksch A, Dini-Andreote F, Schilder M, Chen AJ, Daksa J, Etalo DW, Tessema T, Kuramae EE, Raaijmakers JM, Bouwmeester H, Brady SM (2024). The soilmicrobiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection. Cell Reports. 

Cantó-Pastor A, Kajala K, Shaar-Moshe L, Manzano C, Timilsena P, De Bellis D, Gray S, Holbein J, Yang H, Mohammad S, Nirmal N, Suresh K, Ursache R, Mason GA, Gouran M, West DA, Borowsky AT, Shackel KA, Sinha N, Bailey-Serres J, Geldner N, Li S, Franke RB, Brady SM.  (2024). A suberized exodermis is required for tomato drought tolerance. Nature Plants. 10 

Borowsky, AT and Bailey-Serres, J. (2024). Rewiring gene circuitry for plant improvement. Nature Genetics

Gouran, Mona and Brady, Siobhan M. (2024). The transcriptional integration of environmental cues with root cell type development. Plant Physiology. 

Demirer GS, Gibson DJ, Yue X, Pan K, Elishav E, Khandal H, Horev G, Tarkowská D, Cantó-Pastor A, Kong S, Manzano C, Maloof JN, Savaldi-Goldstein S, Brady SM. (2023). Phosphate deprivation‐induced changes in tomato are mediated by an interaction between brassinosteroid signaling and zinc. New Phytologist. 239 

Reynoso MA, Borowsky AT, Pauluzzi GC, Yeung E, Zhang J, Formentin E, Velasco J, Cabanlit S, Duvenjian C, Prior MJ, Akmakjian GZ, Deal RB, Sinha NR, Brady SM, Girke T, Bailey-Serres J. (2022). Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice. Developmental Cell. 57 

Kawa D and Brady,  SM. (2022). Root cell types as an interface for biotic interactions. Trends in Plant Science. 

Li S and Nakayama H, Sinha, NR (2023). How to utilize comparative transcriptomics to dissect morphological diversity in plants. CurrentOpinion in Plant Biology. 76 

Kajala K, Gouran M, Shaar-Moshe L, Mason GA, Rodriguez-Medina J, Kawa D, Pauluzzi G, Reynoso MA, Canto-Pastor A, Manzano C, Lau V, Artur MAS, West DA, Gray SB, Borowsky AT, Moore BM, Yao AI, Morimoto KW, Bajic M, Formentin E, Nirmal NA, Rodriguez A, Pasha A, Deal RB, Kliebenstein DJ, Hvidsten TR, Provart NJ, Sinha N, Runcie DE, Bailey-Serres J, Brady SM (2021). Innovation, conservation, and repurposing of gene function in root cell type development. Cell

Reynoso MA, Kajala K, Bajic M, West DA, Pauluzzi G, Yao A, Hatch K, Zumstein K, Woodhouse M, Rodriguez-Medina J, Sinha N, Brady SM, Deal RB, Bailey-Serres J (2019). Evolutionary flexibility in flooding response circuitry in angiosperms. Reprint. Science 365: 1291–1295.

Maher K, Bajic M, Kajala K, Reynoso M, Pauluzzi G, West DA, Zumstein K, Woodhouse M, Bubb K, Dorrity M, Queitsch C, Bailey-Serres J, Sinha N, Brady SM, Deal RB (2018). Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules. Plant Cell 30: 15-36.

Bajic M, Maher K, Deal RB (2018). Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq. Plant Chromatin Dynamics 183-201.

Reynoso M, Pauluzzi G, Kajala K, Cabanlit S, Velasco J, Bazin J, Deal RB, Sinha N, Brady SM, Bailey-Serres J (2018). Nuclear transcriptomes at high resolution using retooled INTACT. Plant Physiology 176: 270-281.

Reynoso M, Pauluzzi G, Cabanlit S, Velasco J, Bazin J, Deal RB, Sinha N, Brady SM, Bailey-Serres J, Kajala K (2018). Isolation of Nuclei in Tagged Cell Types (INTACT), RNA Extraction and Ribosomal RNA Degradation to Prepare Material for RNA-Seq. Bio-protocol e2458.

Lee T, Bailey-Serres J (2018). Lighting the shadows: methods that expose nuclear and cytoplasmic gene regulatory control. Curr Opin Biotechnol. 49: 29-34.

Zhao D, Hamilton JP, Hardigan M, Yin D, He T, Vaillancourt B, Reynoso M, Pauluzzi G, Funkhouser S, Cui Y, Bailey-Serres J, Jiang J, Buell CR, Jiang N (2017). Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation. Genes Genomes Genetics 7: 203.

Townsley BT, Covington MF, Ichihashi Y, Zumstein K, Sinha NR (2015). BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction. Front Plant Sci 6: 366.

Mickelbart MV, Hasegawa PM, Bailey-Serres J (2015). Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat Rev Genet 16: 237-51.

Voesenek LA, Bailey-Serres J (2015). Flood adaptive traits and processes: an overview. New Phytol 206: 57-73.

Juntawong P, Hummel M, Bazin J, Bailey-Serres J (2015). Ribosome profiling: a tool for quantitative evaluation of dynamics in mRNA translation. Methods Mol Biol 1284: 139-73.

Reynoso MA, Juntawong P, Lancia M, Blanco FA, Bailey-Serres J, et al (2015). Translating Ribosome Affinity Purification (TRAP) Followed by RNA Sequencing Technology (TRAP-SEQ) for Quantitative Assessment of Plant Translatomes. Methods Mol Biol 1284: 185-207.

Sorenson R, Bailey-Serres J (2015). Rapid Immunopurification of Ribonucleoprotein Complexes of Plants. Methods Mol Biol 1284: 209-19.

Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, et al. (2014). Hairy Root Transformation Using Agrobacterium rhizogenes as a Tool for Exploring Cell Type-Specific Gene Expression and Function Using Tomato as a Model. Plant Physiol 166: 455-69.

Kajala K, Coil DA, Brady SM (2014). Draft Genome Sequence of Rhizobium rhizogenes Strain ATCC 15834. Genome Announc 2(5).