Publications by authors named "Matthieu Heitz"
Spatial Transcriptomics Brings New Challenges and Opportunities for Trajectory Inference.
Annu Rev Biomed Data Sci
November 2024
Spatial transcriptomics (ST) brings new dimensions to the analysis of single-cell data. While some methods for data analysis can be ported over without major modifications, they are the exception rather than the rule. Trajectory inference (TI) methods in particular can suffer from significant challenges due to spatial batch effects in ST data.
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- - Single-cell sequencing offers detailed genomic insights but lacks the spatial context of cells; advancements in spatial transcriptomics and multi-omics technologies aim to bridge this gap by analyzing tissue molecular profiles.
- - The article classifies current spatial genomics technologies into three categories: optical imaging, positional indexing, and mathematical cartography, while discussing their trade-offs, limitations, and potential synergies with single-cell methods.
- - A proposed theoretical framework called DNA-GPS aims to enhance large-scale spatial genomics by integrating concepts from mathematical cartography and positional indexing, potentially allowing for 3D positioning of cells without optical measurements.
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-responsive gene expression specific to different cell types and developmental stages of the root, we identified the elongating cortex as a site where brassinosteroids trigger a shift from proliferation to elongation associated with increased expression of cell wall-related genes. Our analysis revealed () and () as brassinosteroid-responsive transcription factors that regulate cortex cell elongation.
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