Interpretable Histology Analysis
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HOPE: Interpretable Histology Analysis with Spatial Omics-Derived Signatures for Precision Oncology
Hematoxylin and eosin (H&E) stained images are fundamental clinical tools for disease assessment. However, even with advanced computational models, their prognostic capabilities remain limited. Spatial omics characterizes tumor microenvironments (TME) in detail yet remains clinically inaccessible due to cost and complexity.
SciCore-Omics: a tri-modal foundation model unifying histology, spatial transcriptomics and language for spatial biology
Histomorphology and spatial transcriptomics capture complementary aspects of tissue biology, but their relationships remain difficult to extract, align, and interpret at scale. Existing foundation models typically connect histology, omics, or language only pairwise, which limits their capacity to jointly infer molecular states, decode spatial tissue organization, and generate biologically grounded explanations. Here, we show SciCore-Omics, the first tri-modal foundation model linking...
Multivariate integration of histological images and gene expression data: a comparative review
Integrating histological images with gene expression data offers a promising approach for linking tissue morphologies to molecular signatures and improving disease subtyping. However, such integration remains challenging due to the high dimensionality of these datasets, cross-modal heterogeneity, and limited interpretability. Multivariate methods such as Sparse Canonical Correlation Analysis (Sparse CCA), Joint Nonnegative Matrix Factorisation (Joint NMF), and Angle-based Joint and...
Mitochondria directly interact with the nuclear pore complex
Abstract Mitochondria regulate cellular processes through direct and indirect interactions with other organelles. A well-studied example has been contact with the endoplasmic reticulum at mitochondrial-associated endoplasmic reticulum membranes1, which control pathways including redox and calcium homeostasis2,3. Recent studies have also reported direct mitochondria–nuclear membrane contacts in cancer cells and yeast that promote pro-survival signalling4,5.