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Protocol for dual spatial transcriptomic profiling of infected tissues
Dual spatial transcriptomics analysis offers profiling of host- and pathogen-specific transcriptional patterns in infected tissues to establish pathoadaptation signatures and predict infection outcomes. Here, we present a protocol for tissue processing, imaging, selection of regions …
Read PDFEmerging insights into plant disease management: multi-omics approaches elucidate the molecular mechanisms underlying pathogen virulence differentiation in natural populations
A recent study by R. Cheng, T. Lv, P. Ji, B. Ma, et al. (Appl Environ Microbiol 91:e01685-25, 2025, https://doi.org/10.1128/aem.01685-25) used multi-omics analysis to reveal the molecular map of pathogen virulence differentiation driven by natural …
Read PDFThe Role of Neutrophils and NETosis in Diseases: The Implications for Therapy
Neutrophils are the most abundant innate immune cells and are pivotal first responders in host defense, playing an important role in maintaining body homeostasis and regulating pathological conditions. Growing evidence indicates that neutrophils exhibit functional …
Read PDFArtificial intelligence and multiomics integration for Parkinson's disease drug development
Recent advances underscore the potential of integrating multiomics, such as genomics, transcriptomics, proteomics, and metabolomics, and artificial intelligence to overcome limitations regarding early diagnosis and treatment of Parkinson's disease. Developing a comprehensive view of the …
Read PDFA Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application
Biological macromolecules assemble into sophisticated spatial architectures to orchestrate fundamental cellular processes. Understanding this architecture is therefore essential for deciphering the mechanisms of life. Driven by advances in high-throughput sequencing and single-molecule imaging, spatial omics …
Read PDFBenchmarking cell-type-specific spatially variable gene detection methods
Cell-type-specific spatially variable genes (ctSVGs) integrate cell-type composition with spatially varying gene expression, revealing novel insights into molecular mechanisms through spatial transcriptomics. However, the emerging methods devoted to ctSVG detection have not been systematically evaluated, …
Read PDFA new era of precision diagnosis and treatment for lung cancer: artificial intelligence-driven multimodal data integration and clinical applications
Certain characteristics, such as high heterogeneity, a complex tumor microenvironment, metastatic potential, and drug resistance, render Lung cancer (LC) a formidable challenge for clinical management. With rapid advancements in high-throughput sequencing, medical imaging, and digital …
Read PDFOpportunities and challenges in the application of spatiotemporal transcriptomics in plant research
Spatiotemporal heterogeneity is recognized as a key driver of functional diversity in tissues. Spatial transcriptomics, which integrates high-throughput transcriptomics with high-resolution tissue imaging, enables the precise mapping of gene expression patterns at the tissue section …
Read PDFHuman Systems Immunology in the Omics Era: Challenges, Methods, and Emerging Directions
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Read PDFTertiary lymphoid structures in the era of cancer therapy
On September 9th, 2025, the 3rd Workshop on Tertiary lymphoid structures (TLS) took place in Utrecht as pre-meeting to CICON2025. Advances in TLS biology, diversity, and clinical significance are rapidly reshaping the field. The studies …
Read PDFAdvancing chemical mixture toxicity assessment using advanced in vitro NAMs: current status and future perspectives
Chemical exposure in real-world settings occurs predominantly as mixtures, whereas toxicological assessment has long been shaped by single-substance paradigms. As interest in more human-relevant and mechanistically informative testing strategies has grown, new approach methodologies (NAMs) …
Read PDFMulti-Omics Landscape of Circadian Clock Dysregulation Across the Chronic Liver Disease Spectrum
The liver circadian clock coordinates hepatic lipid metabolism, bile acid synthesis, and glucose homeostasis through interlocking transcription-translation feedback loops. Disruption of this temporal organization is increasingly recognized as a shared pathological feature across the chronic …
Read PDFThe gut microbiome in colorectal anastomotic leakage: from mechanisms to precision
Anastomotic leakage after curative colorectal cancer resection remains a frequent and severe complication that increases short-term mortality, worsens long-term oncologic outcomes, and places substantial burdens on individuals and health systems despite advances in surgical technique …
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