Related papers: HEIST: A Graph Foundation Model for Spatial Transc…
The cells and their spatial patterns in the tumor microenvironment (TME) play a key role in tumor evolution, and yet the latter remains an understudied topic in computational pathology. This study, to the best of our knowledge, is among the…
The remarkable success of foundation models has sparked growing interest in their application to single-cell biology. Models like Geneformer and scGPT promise to serve as versatile tools in this specialized field. However, representing a…
Cancer diagnosis, prognosis, and therapeutic response prediction are heavily influenced by the relationship between the histopathological structures and the function of the tissue. Recent approaches acknowledging the structure-function…
The rapid development of spatial transcriptomics (ST) technologies is revolutionizing our understanding of the spatial organization of biological tissues. Current ST methods, categorized into next-generation sequencing-based (seq-based) and…
The rapid development of spatial transcriptomics(ST) enables the measurement of gene expression at spatial resolution, making it possible to simultaneously profile the gene expression, spatial locations of spots, and the matched…
Identifying disease-indicative genes is critical for deciphering disease mechanisms and has attracted significant interest in biomedical research. Spatial transcriptomics offers unprecedented insights for the detection of disease-specific…
Graphs are a central representation in biomedical research, capturing molecular interaction networks, gene regulatory circuits, cell--cell communication maps, and knowledge graphs. Despite their importance, currently there is not a broadly…
Spatial Transcriptomics is a groundbreaking technology that integrates histology images with spatially resolved gene expression profiles. Among the various Spatial Transcriptomics techniques available, Visium has emerged as the most widely…
Spatially resolved transcriptomics represents a significant advancement in single-cell analysis by offering both gene expression data and their corresponding physical locations. However, this high degree of spatial resolution entails a…
Identification and counting of cells and mitotic figures is a standard task in diagnostic histopathology. Due to the large overall cell count on histological slides and the potential sparse prevalence of some relevant cell types or mitotic…
Spatial transcriptomics is an emerging field that enables the identification of functional regions based on the spatial distribution of gene expression. Integrating this functional information present in transcriptomic data with structural…
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…
The advancement of Spatial Transcriptomics (ST) has facilitated the spatially-aware profiling of gene expressions based on histopathology images. Although ST data offers valuable insights into the micro-environment of tumors, its…
Spatial transcriptomics has revolutionized tissue analysis by simultaneously mapping gene expression, spatial topography, and histological context across consecutive tissue sections, enabling systematic investigation of spatial…
Spatial transcriptomics is an emerging technology that aligns histopathology images with spatially resolved gene expression profiling. It holds the potential for understanding many diseases but faces significant bottlenecks such as…
The recent advancement of spatial transcriptomics (ST) allows to characterize spatial gene expression within tissue for discovery research. However, current ST platforms suffer from low resolution, hindering in-depth understanding of…
Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have…
Histopathology, particularly hematoxylin and eosin (H\&E) staining, plays a critical role in diagnosing and characterizing pathological conditions by highlighting tissue morphology. However, H\&E-stained images inherently lack molecular…
Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from their original microenvironments, resulting in a loss of…
Spatial transcriptomics (ST) profiles gene expression across a tissue section while preserving the spatial coordinates. Because current ST technologies typically profile two-dimensional tissue slices, integrating and aligning slices from…