Computational approaches and challenges in spatial transcriptomics
The development of spatial transcriptomics (ST) technologies has transformed genetic
research from a single-cell data level to a two-dimensional spatial coordinate system and …
research from a single-cell data level to a two-dimensional spatial coordinate system and …
[HTML][HTML] Spatial transcriptomics reveals niche-specific enrichment and vulnerabilities of radial glial stem-like cells in malignant gliomas
Y Ren, Z Huang, L Zhou, P Xiao, J Song, P He… - Nature …, 2023 - nature.com
Diffuse midline glioma-H3K27M mutant (DMG) and glioblastoma (GBM) are the most lethal
brain tumors that primarily occur in pediatric and adult patients, respectively. Both tumors …
brain tumors that primarily occur in pediatric and adult patients, respectively. Both tumors …
[HTML][HTML] Padlock Probe–Based Targeted In Situ Sequencing: Overview of Methods and Applications
Elucidating spatiotemporal changes in gene expression has been an essential goal in
studies of health, development, and disease. In the emerging field of spatially resolved …
studies of health, development, and disease. In the emerging field of spatially resolved …
Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows
Abstract The Xenium In Situ platform is a new spatial transcriptomics product
commercialized by 10X Genomics capable of mapping hundreds of transcripts in situ at a …
commercialized by 10X Genomics capable of mapping hundreds of transcripts in situ at a …
Identifying spatial domain by adapting transcriptomics with histology through contrastive learning
Recent advances in spatial transcriptomics have enabled measurements of gene
expression at cell/spot resolution meanwhile retaining both the spatial information and the …
expression at cell/spot resolution meanwhile retaining both the spatial information and the …
Deep learning in single-cell analysis
Single-cell technologies are revolutionizing the entire field of biology. The large volumes of
data generated by single-cell technologies are high dimensional, sparse, and …
data generated by single-cell technologies are high dimensional, sparse, and …
[HTML][HTML] Clustering the cortical laminae: in vivo parcellation
The laminar microstructure of the cerebral cortex has distinct anatomical characteristics of
the development, function, connectivity, and even various pathologies of the brain. In recent …
the development, function, connectivity, and even various pathologies of the brain. In recent …
Insitutype: likelihood-based cell typing for single cell spatial transcriptomics
Accurate cell typing is fundamental to analysis of spatial single-cell transcriptomics, but
legacy scRNA-seq algorithms can underperform in this new type of data. We have …
legacy scRNA-seq algorithms can underperform in this new type of data. We have …
[HTML][HTML] Tissue module discovery in single-cell-resolution spatial transcriptomics data via cell-cell interaction-aware cell embedding
Computational methods are desired for single-cell-resolution spatial transcriptomics (ST)
data analysis to uncover spatial organization principles for how individual cells exert tissue …
data analysis to uncover spatial organization principles for how individual cells exert tissue …
SpatialOne: end-to-end analysis of visium data at scale
Motivation Spatial transcriptomics allow to quantify mRNA expression within the spatial
context. Nonetheless, in-depth analysis of spatial transcriptomics data remains challenging …
context. Nonetheless, in-depth analysis of spatial transcriptomics data remains challenging …