Spatiotemporal omics for biology and medicine

L Liu, A Chen, Y Li, J Mulder, H Heyn, X Xu - Cell, 2024 - cell.com
The completion of the Human Genome Project has provided a foundational blueprint for
understanding human life. Nonetheless, understanding the intricate mechanisms through …

Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data

G Yan, SH Hua, JJ Li - Nature Communications, 2025 - nature.com
In the analysis of spatially resolved transcriptomics data, detecting spatially variable genes
(SVGs) is crucial. Numerous computational methods exist, but varying SVG definitions and …

Dimension-agnostic and granularity-based spatially variable gene identification using BSP

J Wang, J Li, ST Kramer, L Su, Y Chang, C Xu… - Nature …, 2023 - nature.com
Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with
tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene …

Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST

W Liu, X Liao, Z Luo, Y Yang, MC Lau, Y Jiao… - Nature …, 2023 - nature.com
Spatially resolved transcriptomics involves a set of emerging technologies that enable the
transcriptomic profiling of tissues with the physical location of expressions. Although a …

Map** the topography of spatial gene expression with interpretable deep learning

U Chitra, BJ Arnold, H Sarkar, K Sanno, C Ma… - Nature …, 2025 - nature.com
Spatially resolved transcriptomics technologies provide high-throughput measurements of
gene expression in a tissue slice, but the sparsity of these data complicates analysis of …

[HTML][HTML] Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex

L Huuki-Myers, A Spangler, N Eagles, KD Montgomery… - BioRxiv, 2023 - ncbi.nlm.nih.gov
Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular
anatomy of the human dorsolateral prefrontal cortex - PMC Back to Top Skip to main content NIH …

A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex

LA Huuki-Myers, A Spangler, NJ Eagles… - Science, 2024 - science.org
The molecular organization of the human neocortex historically has been studied in the
context of its histological layers. However, emerging spatial transcriptomic technologies …

Evaluating spatially variable gene detection methods for spatial transcriptomics data

C Chen, HJ Kim, P Yang - Genome Biology, 2024 - Springer
Background The identification of genes that vary across spatial domains in tissues and cells
is an essential step for spatial transcriptomics data analysis. Given the critical role it serves …

Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods

N Charitakis, A Salim, AT Piers, KI Watt, ER Porrello… - Genome Biology, 2023 - Springer
Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved
transcriptomics data. SVGs provide biological insights by defining transcriptomic differences …

Spatial Transcriptomics: Biotechnologies, Computational Tools, and Neuroscience Applications

Q Wang, H Zhu, L Deng, S Xu, W **e, M Li… - Small …, 2025 - Wiley Online Library
Spatial transcriptomics (ST) represents a revolutionary approach in molecular biology,
providing unprecedented insights into the spatial organization of gene expression within …