Publications – Shahan Lab

Publications

Pluripotency of a Founding Field: Rebranding Developmental Biology

Rogers CD, Amemiya C, Arur S, Babonis L, Barresi M, Bartlett M, Behringer R, Benham-Pyle B, Bergmann D, Blackman B, Brown CT, Browne B, Camacho J, Chabu CY, Chow I, Cleaver O, Cool J, Dennis MY, Dickinson AJ, Di Talia S, Frank M, Gillmor S, Haag ES, Hariharan I, Harland R, Husbands A, Jerome-Majewska L, Koenig K, Labonne C, Layden M, Lowe C, Mani M, Martik M, McKown K, Moens C, Mosimann C, Onyenedum J, Reed R, Rivera A, Rokhsar D, Royer L, Rutaganira F, Shahan R, Sinha N, Swalla B, Van Norman JM, Wagner DE, Wikramanayake A, Zebell S, Brady SM.

Development. 2024 Feb 1;151(3):dev202342. doi: 10.1242/dev.202342. PMID: 38345109

Best Practices for the Execution, Analysis, and Data Storage of Plant Single Cell/Nucleus Transcriptomics

Grones C, Eekhout T, Shi D, Neumann M, Berg LS, Ke Y, Shahan R, Cox KL Jr, Gomez-Cano F, Nelissen H, Lohmann JU, Giacomello S, Martin OC, Cole B, Wang JW, Kaufmann K, Raissig MT, Palfalvi G, Greb T, Libault M, De Rybel B.

The Plant Cell. 2024 Mar 29;36(4):812-828. doi:10.1093/plcell/koae003. PMID: 38231860

Resolving Plant Development in Space and Time With Single-Cell Genomics.

Nolan TM, Shahan R.

Current Opinion in Plant Biology. 2023 Dec;76:102444. doi: 10.1016/j.pbi.2023.102444. PMID: 37696725

Brassinosteroid Gene Regulatory Networks at Cellular Resolution in the Arabidopsis Root

Nolan TM, Vukašinović N, Hsu CW, 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.

Science. 2023 Mar 31;379(6639):eadf4721. doi: 10.1126/science.adf4721. PMID: 36996230

Protocol for Fast scRNA-seq Raw Data Processing Using scKB and Non-Arbitrary Quality Control with COPILOT

Hsu CW, Shahan R, Nolan TM, Benfey PN, Ohler U

STAR Protocols. 2022 Dec 16;3(4):101729. doi: 10.1016/j.xpro.2022.101729. PMID: 36181683

A Single-Cell Arabidopsis Root Atlas Reveals Developmental Trajectories in Wild-Type and Cell Identity Mutants

Shahan R, Hsu CW, Nolan TM, Cole BJ, Taylor IW, Greenstreet L, Zhang S, Afanassiev A, Vlot AHC, Schiebinger G, Benfey PN, Ohler U

Developmental Cell. 2022 Feb 28;57(4):543-560.e9. doi: 10.1016/j.devcel.2022.01.008. PMID: 35134336

Vision, Challenges and Opportunities for a Plant Cell Atlas

Plant Cell Atlas Consortium; Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JA, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY

Elife. 2021 Sep 7;10:e66877. doi: 10.7554/eLife.66877.PMID: 34491200

Single-Cell Analysis of Cell Identity in the Arabidopsis Root Apical Meristem: Insights and Opportunities

Shahan R, Nolan TM, Benfey PN.

Journal of Experimental Botany. 2021 Oct 13;72(19):6679-6686. doi: 10.1093/jxb/erab228. PMID: 34018001

Tempting Fate: A Guanylate-Binding Protein Maintains Tomato Fruit Cell Differentiation

Shahan R

Plant Cell. 2020 Oct;32(10):3047-3048. doi: 10.1105/tpc.20.00627. Epub 2020 Aug 13.PMID: 32796122

It’s All in the Neighborhood: SHORTROOT-Mediated Intercellular Signals Coordinate Phloem Development in the Root

Shahan R

Plant Cell. 2020 May;32(5):1350-1351. doi: 10.1105/tpc.20.00156. Epub 2020 Mar 4.PMID: 32132130

The Cold Never Bothered Me Anyway: DELLA-Interacting GROWTH REGULATING FACTORS Mediate Plant Growth in Cold Stress.

Shahan R

Plant Cell. 2020 Apr;32(4):797-798. doi: 10.1105/tpc.20.00079. Epub 2020 Feb 14.PMID: 32060177

A Co-opted Regulator of Lateral Root Development Controls Nodule Organogenesis in Lotus.

Shahan R, Benfey PN

Dev Cell. 2020 Jan 6;52(1):6-7. doi: 10.1016/j.devcel.2019.12.009.PMID: 31951556

Father Knows Best? Small RNA Pathway Controls Endosperm Response to Paternal Genomic Dosage.

Shahan R.

Plant Cell. 2019 Jul;31(7):1425-1426. doi: 10.1105/tpc.19.00362. Epub 2019 May 10.PMID: 31076538

Identification of Genes Preferentially Expressed in Wild Strawberry Receptacle Fruit and Demonstration of Their Promoter Activities

Shahan R, Li D, Liu Z.

Horticulture Research. 2019 May 1;6:50. doi: 10.1038/s41438-019-0134-6. PMID: 31044078

The Future is Now: Gene Expression Dynamics at Single Cell Resolution.

Shahan R.

Plant Cell. 2019 May;31(5):933-934. doi: 10.1105/tpc.19.00247. Epub 2019 Apr 12.PMID: 30979794

Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry.

Shahan R, Zawora C, Wight H, Sittmann J, Wang W, Mount SM, Liu Z.

Plant Physiology. 2018 Sep;178(1):202-216. doi: 10.1104/pp.18.00086. PMID: 29991484

Re-Annotation of the Woodland Strawberry (Fragaria Vesca) Genome

Darwish O, Shahan R, Liu Z, Slovin JP, Alkharouf NW.

BMC Genomics. 2015 Jan 27;16(1):29. doi: 10.1186/s12864-015-1221-1. PMID: 25623424

Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria Vesca.

Kang C, Darwish O, Geretz A, Shahan R, Alkharouf N, Liu Z.

The Plant Cell. 2013 Jun;25(6):1960-78. doi: 10.1105/tpc.113.111732. PMID: 23898027