Publications Hsu C.-W., C.-Y. Chen, T.M. Nolan, P.N. Benfey, U. Ohler (2025). GeneSys: Generative Modeling of Developmental System. bioRxiv. https://doi.org/10.1101/2025.08.20.671385 Vučićević D., C.-W. Hsu, L.S.L. Zepeda, M. Burkert, A. Hirsekorn, I. Bilić, N. Kastelić, M. Landthaler, S.A. Lacadie, U. Ohler (2025). Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation. Cell Genomics. https://doi.org/10.1016/j.xgen.2025.100984 Zhu M.*, C.-W. Hsu*, L.L. Peralta Ogorek, I.W. Taylor, S. La Cavera, D.M. Oliveira, L. Verma, P. Mehra, M. Mijar, A. Sadanandom, F. Perez-Cota, W. Boerjan, T.M. Nolan, M.J. Bennett, P.N. Benfey, B.K. Pandey (2025). Single-cell transcriptomics reveal how root tissues adapt to soil stress. Nature 642, 721–729. https://doi.org/10.1038/s41586-025-08941-z Vukašinović N.*, C.-W. Hsu*, M. Marconi, S. Li, C. Zachary, R. Shahan, P. Szekley, Z. Aardening, I. Vanhoutte, Q. Ma, L. Pinto, P. Krupař, N. German, J. Zhang, C. Simon, J. Perez-Sancho, P. C. Quijada, Q. Zhou, L.R. Lee, J. Cai, E.M. Bayer, M. Fendrych, E. Truernit, Y. Zhou, S. Savaldi-Goldstein, K. Wabnik, T.M. Nolan, E. Russinova (2025). Polarity-guided uneven mitotic divisions control brassinosteroid activity in proliferating plant root cells. Cell 188 (8), 2063-2080. e24. https://doi.org/10.1016/j.cell.2025.02.011 Taylor I.W., O.R. Patharkar, M. Mijar, C.-W. Hsu, J. Baer, C.E. Niederhuth, U. Ohler, P.N. Benfey, J.C. Walker (2024). Arabidopsis uses a molecular grounding mechanism and a biophysical circuit breaker to limit floral abscission signaling. Proceedings of the National Academy of Sciences 121 (44) e2405806121 https://doi.org/10.1073/pnas.2405806121 Blanco-Touriñán N., S. Rana, T.M. Nolan, K. Li, N. Vukašinović, C.-W. Hsu, E. Russinova, C.S. Hardtke. (2024). The brassinosteroid receptor gene BRI1 safeguards cell-autonomous brassinosteroid signaling across tissues. Science advances. https://doi: 10.1126/sciadv.adq3352 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 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 Shahan, R.*, C.-W. 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 Carley, L.N., J.P. Mojica, B. Wang, C.-Y. Chen, Y.-P. Lin, K. Prasad, E. Chan, C.-W. Hsu, R. Keith, C.L. Nuñez, C.F. Olson-Manning, C.A. Rushworth, M.R. Wagner, J. Wang, P.-M. Yeh, M. Reichelt, K. Ghattas, J. Gershenzon, C.-R. Lee, T. Mitchell-Olds. (2021). Ecological factors influence balancing selection on leaf chemical profiles of a wildflower. Nature ecology & evolution 5 (8), 1135-1144. https://doi.org/10.1038/s41559-021-01486-0 Hsu, C.-W., C. Lo and C. Lee. (2019). On the post‐glacial spread of human commensal Arabidopsis thaliana: journey to the east. New Phytologist 222 (3), 1447-1457. https://doi:10.1111/nph.15682 Check out my published tools
