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Rachel Shahan


Selected Publications

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.

Journal Article The Plant cell · March 2024 Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcripti ... Full text Cite

Resolving plant development in space and time with single-cell genomics.

Journal Article Current opinion in plant biology · December 2023 Single-cell genomics technologies are ushering in a new research era. In this review, we summarize the benefits and current challenges of using these technologies to probe the transcriptional regulation of plant development. In addition to profiling cells ... Full text Cite

Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root.

Journal Article Science (New York, N.Y.) · March 2023 Brassinosteroids are plant steroid hormones that regulate diverse processes, such as cell division and cell elongation, through gene regulatory networks that vary in space and time. By using time series single-cell RNA sequencing to profile brassinosteroid ... Full text Cite

Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.

Journal Article STAR protocols · December 2022 We describe a protocol to perform fast and non-arbitrary quality control of single-cell RNA sequencing (scRNA-seq) raw data using scKB and COPILOT. scKB is a wrapper script of kallisto and bustools for accelerated alignment and transcript count matrix gene ... Full text Open Access Cite

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.

Journal Article Developmental cell · February 2022 In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying d ... Full text Cite

Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities.

Journal Article Journal of experimental botany · October 2021 A fundamental question in developmental biology is how the progeny of stem cells become differentiated tissues. The Arabidopsis root is a tractable model to address this question due to its simple organization and defined cell lineages. In particular, the ... Full text Cite

Editor profile: Siobhan M. Brady.

Journal Article The Plant cell · May 2021 Full text Cite

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

Journal Article Developmental cell · January 2020 Legumes, a subset of flowering plants, form root nodules in symbiosis with nitrogen-fixing bacteria. The regulatory network controlling nodule formation has remained mysterious. In a recent issue of Science, Soyano et al. (2019) demonstrate that co-option ... Full text Cite

A single cellArabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants

Journal Article · 2020 Summary Cell fate acquisition is a fundamental developmental process in all multicellular organisms. Yet, much is unknown regarding how a cell traverses the pathway from stem cell to terminal differentiation. Advances in single cell genomics 1 hol ... Full text Cite

Identification of genes preferentially expressed in wild strawberry receptacle fruit and demonstration of their promoter activities.

Journal Article Horticulture research · January 2019 Fragaria vesca (F. vesca), the wild strawberry, is a diploid model for the commercial, octoploid strawberry as well as other members of the economically relevant Rosaceae family. Unlike the fruits of tomato and Arabidopsis, the ... Full text Cite

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

Journal Article Plant physiology · September 2018 The diploid strawberry, Fragaria vesca, is a developing model system for the economically important Rosaceae family. Strawberry fleshy fruit develops from the floral receptacle and its ripening is nonclimacteric. The external seed configuration of s ... Full text Cite

Re-annotation of the woodland strawberry (Fragaria vesca) genome.

Journal Article BMC genomics · January 2015 BackgroundFragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry. It is native to temperate regions of Eurasia and North America and while it produces edible fruits, it is most highly useful a ... Full text Cite

Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca.

Journal Article The Plant cell · June 2013 Fragaria vesca, a diploid woodland strawberry with a small and sequenced genome, is an excellent model for studying fruit development. The strawberry fruit is unique in that the edible flesh is actually enlarged receptacle tissue. The true fruit are the nu ... Full text Cite