[HTML][HTML] Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges

M Cheng, Y Jiang, J Xu, AFA Mentis, S Wang… - Journal of Genetics and …, 2023 - Elsevier
The ability to explore life kingdoms is largely driven by innovations and breakthroughs in
technology, from the invention of the microscope 350 years ago to the recent emergence of …

[HTML][HTML] Spatial transcriptomics: Technologies, applications and experimental considerations

Y Wang, B Liu, G Zhao, YJ Lee, A Buzdin, X Mu, J Zhao… - Genomics, 2023 - Elsevier
The diverse cell types of an organ have a highly structured organization to enable their
efficient and correct function. To fully appreciate gene functions in a given cell type, one …

[HTML][HTML] Spatial epigenome–transcriptome co-profiling of mammalian tissues

D Zhang, Y Deng, P Kukanja, E Agirre, M Bartosovic… - Nature, 2023 - nature.com
Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics,
are becoming powerful tools for profiling of cellular states in the tissue context,,,–. However …

Molecularly defined and spatially resolved cell atlas of the whole mouse brain

M Zhang, X Pan, W Jung, AR Halpern, SW Eichhorn… - Nature, 2023 - nature.com
In mammalian brains, millions to billions of cells form complex interaction networks to enable
a wide range of functions. The enormous diversity and intricate organization of cells have …

[HTML][HTML] Integrated multimodal cell atlas of Alzheimer's disease

MI Gabitto, KJ Travaglini, VM Rachleff, ES Kaplan… - Nature …, 2024 - nature.com
Alzheimer's disease (AD) is the leading cause of dementia in older adults. Although AD
progression is characterized by stereotyped accumulation of proteinopathies, the affected …

Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex

A Chen, Y Sun, Y Lei, C Li, S Liao, J Meng, Y Bai, Z Liu… - Cell, 2023 - cell.com
Elucidating the cellular organization of the cerebral cortex is critical for understanding brain
structure and function. Using large-scale single-nucleus RNA sequencing and spatial …

SODB facilitates comprehensive exploration of spatial omics data

Z Yuan, W Pan, X Zhao, F Zhao, Z Xu, X Li, Y Zhao… - Nature …, 2023 - nature.com
Spatial omics technologies generate wealthy but highly complex datasets. Here we present
Spatial Omics DataBase (SODB), a web-based platform providing both rich data resources …

SCS: cell segmentation for high-resolution spatial transcriptomics

H Chen, D Li, Z Bar-Joseph - Nature methods, 2023 - nature.com
Spatial transcriptomics promises to greatly improve our understanding of tissue organization
and cell–cell interactions. While most current platforms for spatial transcriptomics only offer …

Spatial transcriptomics reveals the distinct organization of mouse prefrontal cortex and neuronal subtypes regulating chronic pain

A Bhattacherjee, C Zhang, BR Watson… - Nature …, 2023 - nature.com
The prefrontal cortex (PFC) is a complex brain region that regulates diverse functions
ranging from cognition, emotion and executive action to even pain processing. To decode …

Benchmarking spatial clustering methods with spatially resolved transcriptomics data

Z Yuan, F Zhao, S Lin, Y Zhao, J Yao, Y Cui… - Nature …, 2024 - nature.com
Spatial clustering, which shares an analogy with single-cell clustering, has expanded the
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …