General 1 — Trevor M Nolan

* indicates co-first authors

30. Nolan, T.M.*, and R. Shahan*. (2023). Resolving plant development in space and time with single-cell genomics. Invited review, Current Opinion in Plant Biology. https://doi.org/10.1016/j.pbi.2023.102444

29. Nolan, T.M.*, N. Vukasinovic*, C.W. Hsu*, J. Zhang, I. Vanhoutte, R. Shahan, I. Taylor, L. Greenstreet, M. Heitz, A. Afanassiev, P. Wang, P. Szekely, A.Brosnan, Y. Yin, G. Schiebinger, U. Ohler, E. Russinova and P.N. Benfey. (2023). Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root. Science. https://doi.org/10.1126/science.adf4721

28. Wang., Y, J. Perez-Sancho, M. Platre, B.Callebaut, M. Smokvarska, K.Ferrer, Y.Luo, T. Sato, T.M.Nolan, P.Benfey, W. Busch, M. Kvasnica, J. Winne, E. Bayer, N. Vukainovi and E. Russinova. (2023). Plasmodesmata mediate cell-to-cell transport of brassinosteroid hormones. Nature Chemical Biology. https://doi.org/10.1038/s41589-023-01346-x

27. Hsu, C.-W., R. Shahan, T.M. Nolan, P.N. Benfey, and U. Ohler. (2022). Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT. STAR Protocols 3, 101729. https://doi.org/10.1016/j.xpro.2022.101729.

26. Liao, C.-Y.*, Y. Pu*, T.M. Nolan*, C. Montes, H. Guo, J. Walley, Y. Yin, and D.C. Bassham. (2022). Brassinosteroids modulate autophagy through phosphorylation of RAPTOR1B by the GSK3-like kinase BIN2 in Arabidopsis. Autophagy 118. https://doi.org/10.1080/15548627. 2022.2124501

25. Montes, C., P. Wang, C. Liao, T.M. Nolan, G. Song, N. Clark, J. Elmore, H. Guo, D. Bassham, Y. Yin, and J. Walley. (2022). Integration of multi-omics data reveals interplay between brassinosteroid and TORC signaling in Arabidopsis. New Phytologist. https://doi.org/10.1111/nph. 18404

24. Wang, P., N. Clark, T.M. Nolan, G. Song, P. Bartz, C. Liao, C. Montes-Serey, E. Katz, J. Polko, J. Kieber, D. Kliebenstein, D. Bassham, J. Walley, Y. Yin, and H. Guo. (2022). Integrated omics reveal novel functions and underlying mechanisms of the receptor kinase FERONIA in Arabidopsis thaliana. The Plant Cell. https://doi.org/10.1093/plcell/koac111

23. Wang, P., N. Clark, T.M. Nolan, G. Song, O. Whitham, C-Y. Liao, C. Montes-Serey, D.C. Bassham, J. Walley, Y. Yin, Y and H. Guo (2022). FERONIA functions through Target of Rapamycin (TOR) to negatively regulate autophagy. Front. Plant Sci. 13, 961096. https: //doi.org/10.3389/fpls.2022.961096.

22. Shahan,R., C. Hsu, T.M. Nolan, B. Cole, I. Taylor, L. Greenstreet, S. Zhang, A. Afanassiev, A. Hendrika C. Vlot, G. Schiebinger, P.N. Benfey, and U. Ohler. (2022). A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Developmental Cell. 57 (4), 543-560. e9 https://doi.org/10.1016/j.devcel.2022.01.008 • On the cover of Developmental Cell.

21. Wang, P., T.M. Nolan, N. Clark, H. Jiang, C. Montes-Serey, H. Guo, D. Bassham, J. Wal- ley, and Y. Yin. (2021). The F-box E3 ubiquitin ligase BAF1 mediates the degradation of the brassinosteroid-activated transcription factor BES1 through selective autophagy in Arabidopsis. The Plant Cell. 33 (11), 3532-3554 https://doi.org/10.1093/plcell/koab210

20. Shahan, R., T.M. Nolan and P.N. Benfey. (2021). Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities. Journal of experimental botany. 72 (19), 6679-6686 https://doi.org/10.1093/jxb/erab228

19. Clark N., T.M. Nolan, P. Wang, G. Song, C. Montes, C. Valentine, H. Guo, R. Sozzani, Y.Yin, and J. Walley. (2021). Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis. Nature communications. 12 (1), 1-13 https://doi.org/10. 1038/s41467-021-26165-3

18. Xiang, L.*, T.M. Nolan*, Y. Bao, M. Elmore, T. Tuel, J. Gai, D. Shah, P. Wang, N. Huser, A.Hurd, S.McLaughlin, S.Howell, J.Walley, Y. Yin, and L. Tang. (2021). Robotic Assay for Drought (RoAD): an automated phenotyping system for brassinosteroid and drought responses. The Plant Journal. 107 (6), 1837-1853. https://https://doi.org/10.1111/tpj.15401

17. Nolan, T.M., N. Vukasinovic, D. Liu, J. Russinova and Y. Yin. (2020). Brassinosteroids: Multidimensional Regulators of Plant Growth, Development and Stress Responses. Plant Cell. 32 (2), 295-318. https://doi.org/10.1105/tpc.19.00335

16. Jiang, H., B. Tang, Z. Xie, T.M. Nolan, H. Ye, G. Song, J. Walley and Y. Yin. (2019). GSK3- Like Kinase BIN2 Phosphorylates RD26 to Potentiate Drought Signaling in Arabidopsis. The Plant Journal. https://doi.org/10.1111/tpj.14484

15. Xie, Z., T.M. Nolan, H. Jiang, B. Tang, M, Zhang, Z. Li and Y. Yin. (2019). The AP2/ERF Transcription Factor TINY Modulates Brassinosteroid-Regulated Plant Growth and Drought Response in Arabidopsis. Plant Cell. 31 (8), 1788-1806. https://doi.org/10.1105/tpc.18.00918

14. Wang, P., T.M. Nolan, Y. Yin and D. Bassham. (2019). Identification of a transcription factor-centered regulatory network of autophagy genes in Arabidopsis. Autophagy. 1-17. https: //doi.org/10.1080/15548627.2019.1598753

13. Xie, Z., T.M. Nolan, H. Jiang and Y. Yin. (2019). AP2/ERF Transcription Factor Regulatory Networks in Hormone and Abiotic Stress Responses in Arabidopsis. Frontiers in Plant Science. 10, 228. https://doi.org/10.3389/fpls.2019.00228

12. Guo, H., T.M. Nolan, Z. Xie, G. Song, J. Walley and Y. Yin. (2018). FERONIA Receptor Kinase Contributes to Plant Immunity by Suppressing Jasmonic Acid Signaling in Arabidopsis thaliana. Current Biology. 28 (20), 3316-3324. https://doi.org/10.1016/j.cub.2018.07.078

11. Nolan, T.M., J. Chen, and Y. Yin. (2017). Cross-talk of Brassinosteroid signaling in controlling growth and stress responses. Biochemical Journal. 474 (16), 2641-2661. https://doi.org/10. 1042/BCJ20160633

10. Chen, J., T.M. Nolan, H. Ye, M. Zhang, H. Tong, P. Xin, J. Chu, C. Chu, Z. Li, and Y. Yin. (2017). Arabidopsis WRKY46, WRKY54 and WRKY70 Transcription Factors Are Involved in Brassinosteroid-Regulated Plant Growth and Drought Response. Plant Cell. 29 (6), 1425- 1439. https://doi.org/10.1105/tpc.17.00364

9. Nolan, T.M., B. Brennan, M. Zhang, M. Yang, J. Chen, M. Zhang, Z. Li, X. Wang, D. Bassham, J. Walley, and Yin, Y. (2017). Selective Autophagy of BES1 Mediated by DSK2 Balances Plant Growth and Survival. Developmental Cell. 41 (1), 33-46. https://doi.org/10.1016/j.devcel. 2017.03.013 • Featured in Science Signaling, BioTechniques, ScieneDaily and Iowa Farmer Today.

8. Yang, M., C. Li, Z. Cia, Y. Hu, T.M. Nolan, F. Yu, Y. Yin, Q. Xie, G. Tang and X. Wang. (2017). SINAT E3 ligases control the light-mediated stability of the brassinosteroid-activated transcription factor BES1 in Arabidopsis. Developmental Cell. 41 (1), 47-58. https://doi.org/ 10.1016/j.devcel.2017.03.014

7. Ye, H., S. Liu, B. Tang, J. Chen, Z. Xie, T.M. Nolan, H. Jiang, H. Guo, H. Lin, L. Li, Y. Wang, H. Tong, M. Zhang, C. Chu, Z. Li, M. Aluru, S. Aluru, P. Schnable and Y. Yin. (2017). RD26 mediates crosstalk between drought and Brassinosteroid signaling pathways. Nature Communications. 8, 14573. https://doi.org/10.1038/ncomms14573

6. Jiang, H., X. Want, T.M. Nolan, Y. Yin, M. Aluru and L. Dong. (2017). Automated microfluidic plant chips-based plant phenotyping system. IEEE 12th International Conference on Nano/Micro Engineered and Molecular Systems (NEMS). 756-760. https://doi.org/10.1109/NEMS.2017. 8017129

5. Nolan, T.M., H. Guo, S. Liu, L. Li, P. Schnable, and Y. Yin. (2016). Identification of Brassinosteroid Target Genes by Chromatin Immunoprecipitation Followed by High-throughput Sequencing (ChIP-seq) and RNA-seq. Brassinosteroid Analysis Book. https://doi.org/10.1007/978-1-4939-6813-8_7

4. Pogorelko, G., S. Kambakam, T.M. Nolan, A. Foudree, O. Zabotina and S. Rodermel. (2016). Impaired Chloroplast Biogenesis in Immutans, an Arabidopsis Variegation Mutant, Modifies Developmental Programming, Cell Wall Composition and Resistance to Pseudomonas syringae. Plos one. 11, 4. https://dx.doi.org/10.1371%2Fjournal.pone.0150983

3. Wang, X., J. Chen, Z Xie, S Liu, T.M. Nolan, H. Ye, M. Zhang, H. Guo, P. Schnable, Z. Li, and Y. Yin. (2014). Histone Lysine Methyltransferase SDG8 Is Involved in Brassinosteroid-Regulated Gene Expression in Arabidopsis thaliana. Molecular Plant 7, 1303-1315. https: //doi.org/10.1093/mp/ssu056

2. Putarjunan, A., X. Liu , T.M. Nolan, F. Yu , and S. Rodermel. (2013). Understanding chloroplast biogenesis using second-site suppressors of immutans and var2. Photosynthesis Research 116, 437-453. https://doi.org/10.1007/s11120-013-9855-9

1. Foudree, A., A. Putarjunan, S. Kambakam, T.M. Nolan, J. Fussell, G. Pogorelko, and S. Rodermel. (2012). The Mechanism of Variegation in immutans Provides Insight into Chloroplast Biogenesis. Frontiers in Plant Science 3, 260. https://doi.org/10.3389/fpls.2012.00260

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