@misc{schwartz_peters_hunt_abdul-matin_broeck_sozzani_2021, title={Divide and Conquer: The Initiation and Proliferation of Meristems}, volume={40}, ISSN={["1549-7836"]}, url={http://dx.doi.org/10.1080/07352689.2021.1915228}, DOI={10.1080/07352689.2021.1915228}, abstractNote={Abstract In contrast to animals, which complete organogenesis early in their development, plants continuously produce organs, and structures throughout their entire lifecycle. Plants achieve the continuous growth of organs through the initiation and maintenance of meristems that populate the plant body. Plants contain two apical meristems, one at the shoot and one root, to produce the lateral organs of the shoot and the cell files of the root, respectively. Additional meristems within the plant produce branches while others produce the cell types within the vasculature system. Throughout development, plants must balance producing organs and maintaining their meristems, which requires tightly controlled regulations. This review focuses on the various plant meristems, how cells within these meristems maintain their identity, and particularly the molecular players that regulate stem cell maintenance. In addition, we summarize cell types which share molecular features with meristems, but do not follow the same rules regarding maintenance, including pericycle and rachis founder cells. Together, these populations of cells contribute to the entire organogenesis of plants.}, number={2}, journal={CRITICAL REVIEWS IN PLANT SCIENCES}, publisher={Informa UK Limited}, author={Schwartz, Michael F. and Peters, Rachel and Hunt, Aitch M. and Abdul-Matin, Abdul-Khaliq and Broeck, Lisa and Sozzani, Rosangela}, year={2021}, month={Mar}, pages={147–156} }
 @article{spurney_schwartz_gobble_sozzani_broeck_2021, title={Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification}, volume={2328}, ISBN={["978-1-0716-1533-1"]}, ISSN={["1940-6029"]}, DOI={10.1007/978-1-0716-1534-8_4}, abstractNote={Gene expression data analysis and the prediction of causal relationships within gene regulatory networks (GRNs) have guided the identification of key regulatory factors and unraveled the dynamic properties of biological systems. However, drawing accurate and unbiased conclusions requires a comprehensive understanding of relevant tools, computational methods, and their workflows. The topics covered in this chapter encompass the entire workflow for GRN inference including: (1) experimental design; (2) RNA sequencing data processing; (3) differentially expressed gene (DEG) selection; (4) clustering prior to inference; (5) network inference techniques; and (6) network visualization and analysis. Moreover, this chapter aims to present a workflow feasible and accessible for plant biologists without a bioinformatics or computer science background. To address this need, TuxNet, a user-friendly graphical user interface that integrates RNA sequencing data analysis with GRN inference, is chosen for the purpose of providing a detailed tutorial.}, journal={MODELING TRANSCRIPTIONAL REGULATION}, author={Spurney, Ryan and Schwartz, Michael and Gobble, Mariah and Sozzani, Rosangela and Broeck, Lisa}, year={2021}, pages={47–65} }