Scholars@Duke

• Research
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  Selected Grants

  • Architecture and Dynamics of the Gene Regulatory Network Controlling Cell Fate awarded by National Institutes of Health 2020 - 2022
• Publications & Artistic Works
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  Selected Publications

  • Academic Articles

    • Nolan, Trevor M., Nemanja Vukašinović, Che-Wei Hsu, Jingyuan Zhang, Isabelle Vanhoutte, Rachel Shahan, Isaiah W. Taylor, et al. “Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root.” Science (New York, N.Y.) 379, no. 6639 (March 2023): eadf4721. https://doi.org/10.1126/science.adf4721.
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    • Hsu, Che-Wei, Rachel Shahan, Trevor M. Nolan, Philip N. Benfey, and Uwe Ohler. “Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.” Star Protocols 3, no. 4 (December 2022): 101729. https://doi.org/10.1016/j.xpro.2022.101729.
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    • Shahan, Rachel, Che-Wei Hsu, Trevor M. Nolan, Benjamin J. Cole, Isaiah W. Taylor, Laura Greenstreet, Stephen Zhang, et al. “A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.” Developmental Cell 57, no. 4 (February 2022): 543-560.e9. https://doi.org/10.1016/j.devcel.2022.01.008.
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    • Shahan, Rachel, Trevor M. Nolan, and Philip N. Benfey. “Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities.” Journal of Experimental Botany 72, no. 19 (October 2021): 6679–86. https://doi.org/10.1093/jxb/erab228.
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    • Shahan, Rachel. “Editor profile: Siobhan M. Brady.” The Plant Cell 33, no. 3 (May 2021): 441–44. https://doi.org/10.1093/plcell/koaa050.
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    • Shahan, Rachel. “Tempting Fate: A Guanylate-Binding Protein Maintains Tomato Fruit Cell Differentiation.” The Plant Cell 32, no. 10 (October 2020): 3047–48. https://doi.org/10.1105/tpc.20.00627.
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    • Shahan, Rachel. “It's All in the Neighborhood: SHORTROOT-Mediated Intercellular Signals Coordinate Phloem Development in the Root.” The Plant Cell 32, no. 5 (May 2020): 1350–51. https://doi.org/10.1105/tpc.20.00156.
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    • Shahan, Rachel. “The Cold Never Bothered Me Anyway: DELLA-Interacting GROWTH REGULATING FACTORS Mediate Plant Growth in Cold Stress.” The Plant Cell 32, no. 4 (April 2020): 797–98. https://doi.org/10.1105/tpc.20.00079.
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    • Shahan, Rachel, and Philip N. Benfey. “A Co-opted Regulator of Lateral Root Development Controls Nodule Organogenesis in Lotus.” Developmental Cell 52, no. 1 (January 2020): 6–7. https://doi.org/10.1016/j.devcel.2019.12.009.
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    • Shahan, Rachel, Che-Wei Hsu, Trevor Nolan, Benjamin Cole, Isaiah Taylor, Anna Hendrika Cornelia Vlot, Philip Benfey, and Uwe Ohler. “A single cellArabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants,” 2020. https://doi.org/10.1101/2020.06.29.178863.
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    • Shahan, Rachel. “Father Knows Best? Small RNA Pathway Controls Endosperm Response to Paternal Genomic Dosage.” The Plant Cell 31, no. 7 (July 2019): 1425–26. https://doi.org/10.1105/tpc.19.00362.
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    • Shahan, Rachel. “The Future is Now: Gene Expression Dynamics at Single Cell Resolution.” The Plant Cell 31, no. 5 (May 2019): 933–34. https://doi.org/10.1105/tpc.19.00247.
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    • Shahan, Rachel, Dongdong Li, and Zhongchi Liu. “Identification of genes preferentially expressed in wild strawberry receptacle fruit and demonstration of their promoter activities.” Horticulture Research 6 (January 2019): 50. https://doi.org/10.1038/s41438-019-0134-6.
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    • Shahan, Rachel, Christopher Zawora, Haley Wight, John Sittmann, Wanpeng Wang, Stephen M. Mount, and Zhongchi Liu. “Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry.” Plant Physiology 178, no. 1 (September 2018): 202–16. https://doi.org/10.1104/pp.18.00086.
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    • Darwish, Omar, Rachel Shahan, Zhongchi Liu, Janet P. Slovin, and Nadim W. Alkharouf. “Re-annotation of the woodland strawberry (Fragaria vesca) genome.” Bmc Genomics 16 (January 2015): 29. https://doi.org/10.1186/s12864-015-1221-1.
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    • Kang, Chunying, Omar Darwish, Aviva Geretz, Rachel Shahan, Nadim Alkharouf, and Zhongchi Liu. “Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca.” The Plant Cell 25, no. 6 (June 2013): 1960–78. https://doi.org/10.1105/tpc.113.111732.
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