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Plants contain a large number of cell types and exhibit complex regulatory mechanisms. Studies at the single-cell level have gradually become more common in plant science. Single-cell transcriptomics, spatial transcriptomics, and spatial metabolomics techniques have been combined to analyze plant development. These techniques have been used to study the transcriptomes and metabolomes of plant tissues at the single-cell level, enabling the systematic investigation of gene expression and metabolism in specific tissues and cell types during defined developmental stages. In this review, we present an overview of significant breakthroughs in spatial multi-omics in plants, and we discuss how these approaches may soon play essential roles in plant research.
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http://dx.doi.org/10.1016/j.xplc.2022.100508 | DOI Listing |
PLoS Comput Biol
September 2025
OmnibusXLab, OmnibusX Company Limited, Ho Chi Minh City, Vietnam.
OmnibusX is an integrated, privacy-centric platform that enables code-free multi-omics data analysis by bridging computational methodologies with user-friendly interfaces. Designed to overcome challenges posed by fragmented analytical tools and high computational barriers, OmnibusX consolidates workflows for diverse technologies - including bulk RNA-seq, single-cell RNA-seq, single-cell ATAC-seq, and spatial transcriptomics - into a single, cohesive application. The application integrates established open-source tools such as Scanpy, DESeq2, SciPy, and scikit-learn into transparent, reproducible pipelines, offering users control over analytical parameters.
View Article and Find Full Text PDFOncol Res
September 2025
Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
Studies have reported the special value of PANoptosis in cancer, but there is no study on the prognostic and therapeutic effects of PANoptosis in bladder cancer (BLCA). This study aimed to explore the role of PANoptosis in BLCA heterogeneity and its impact on clinical outcomes and immunotherapy response while establishing a robust prognostic model based on PANoptosis-related features. Gene expression profiles and clinical data were collected from public databases.
View Article and Find Full Text PDFNanoscale
September 2025
Department of Bioengineering & Nano-Bioengineering, Research Center for Bio Materials and Process Development, Incheon National University, Incheon 22012, Republic of Korea.
Rolling circle amplification (RCA) has emerged as a highly versatile and robust isothermal amplification technology, offering exceptional sensitivity, specificity, and scalability for next-generation molecular diagnostics and multi-omics research. Its ability to generate long, repetitive DNA sequences with high fidelity has made it a pivotal tool in disease diagnostics, genomic analysis, and spatial transcriptome profiling. Recent advancements have expanded RCA into various formats, including solution-phase, solid-phase, hydrogel-based, and digital RCA, enhancing its analytical performance and adaptability across diverse biological applications.
View Article and Find Full Text PDFConnect Tissue Res
September 2025
Research Unit of Health Sciences and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland.
Osteoarthritis (OA) is a multifactorial, mechano-inflammatory joint disorder characterized by cartilage degradation, synovial inflammation, and subchondral bone remodeling. Despite its high prevalence and significant impact on quality of life, no disease-modifying treatments have been approved. In many other disease areas, advanced omics technologies are impacting the development of advanced therapies.
View Article and Find Full Text PDFPhytomedicine
August 2025
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China. Electronic address:
Background: Traditional Chinese medicines (TCMs) have a long-standing history and diverse applications. However, their complex multi-component compositions and intricate mechanisms of action pose significant challenges for modern scientific investigation. Addressing these complexities requires advanced techniques capable of dissecting cellular and molecular interactions with high resolution.
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