Research Interests

The proper formation and function of an organ requires cells with distinct characteristics. However, cells from both animals and plants can be reprogrammed to ‘forget’ their original identity and acquire a new fate. Cell fate plasticity is particularly important in plants because it enables the production of new organs. Plant embryo formation produces only a rudimentary body consisting of a root, stem, and a few leaves. The body plan is elaborated post-embryonically by the exquisite branching of roots and shoots. Understanding organ neogenesis in plants has broad implications ranging from regeneration to agriculture and plant-based mitigation strategies for climate change.

My lab combines cutting edge genetic, genomic, and imaging approaches to investigate how distinct cell types and cell states contribute to elaboration of the plant body plan. Specifically, we want to understand 1) what specifies cell identity and 2) how a cell can change its fate or state in response to intrinsic and extrinsic cues. Our long-term goal is to understand how cell fate is programmed to initiate the formation of new tissues and organs in different developmental and environmental contexts.

Selected Publications

Nolan TM and Shahan R (2023) Resolving plant development in space and time with single-cell genomics. Current Opinion in Plant Biology. 76:102444. DOI: 10.1016/j.pbi.2023.102444.

Nolan TM, Vukasinovic N, Hsu C-W, Zhang J, Vanhoutte I, Shahan R, Taylor IW, Greenstreet L, Heitz M, Afanassiev A, Wang P, Szekely P, Brosnan A, Yin Y, Schiebinger G, Ohler U, Russinova E, Benfey PN (2023) Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root. Science. 31; 379 (6639). DOI: 10.1126/science.adf4721.

Shahan R, Hsu C-W, Nolan TM, Cole BJ, Taylor IW, Greenstreet L, Zhang S, Afanassiev A, Vlot AHC, Schiebinger G, Benfey PN, Ohler U (2022) A single cell Arabidopsis root atlas reveals developmental trajectories in wild type and cell identity mutants. Developmental Cell. 57(4): 543-560. DOI: 10.1016/j.devcel.2022.01.008.

Hsu C-W, Shahan R, Nolan TM, Benfey PN, Ohler U (2022) Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT. STAR Protocols. 3(4):101729. DOI: 10.1016/j.xpro.2022.101729.

Shahan R, Li D, and Liu Z (2019) Identification of genes preferentially expressed in wild strawberry receptacle fruit and demonstration of their promoter activities. Horticulture Research. 6:50.   

Shahan R, Zawora C, Sittmann J, Wight H, Wang W, Mount S, and Liu Z (2018) Consensus co-expression network analysis identifies key regulators of flower and fruit development in wild strawberry. Plant Physiology. 178(1): 202-216.

Darwish O, Shahan R, Liu Z, Slovin JP, Alkharouf N (2015) Reannotation of the woodland strawberry (Fragaria vesca) genome. BMC Genomics. 16(1):29.

Kang C, Darwish O, Geretz A, Shahan R, Alkharouf N, Liu Z (2013) Genome-scale transcriptomic insights into early stage fruit development in woodland strawberry Fragaria vesca. The Plant Cell. 25(6):1960-1978.