Spatiotemporal omics for biology and medicine
The completion of the Human Genome Project has provided a foundational blueprint for
understanding human life. Nonetheless, understanding the intricate mechanisms through …
understanding human life. Nonetheless, understanding the intricate mechanisms through …
Streamlining spatial omics data analysis with Pysodb
Advances in spatial omics technologies have improved the understanding of cellular
organization in tissues, leading to the generation of complex and heterogeneous data and …
organization in tissues, leading to the generation of complex and heterogeneous data and …
SpatialData: an open and universal data framework for spatial omics
Spatially resolved omics technologies are transforming our understanding of biological
tissues. However, the handling of uni-and multimodal spatial omics datasets remains a …
tissues. However, the handling of uni-and multimodal spatial omics datasets remains a …
Benchmarking spatial clustering methods with spatially resolved transcriptomics data
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 …
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …
The 2022 Nucleic Acids Research database issue and the online molecular biology database collection
DJ Rigden, XM Fernández - Nucleic acids research, 2022 - academic.oup.com
Abstract The 2022 Nucleic Acids Research Database Issue contains 185 papers, including
87 papers reporting on new databases and 85 updates from resources previously published …
87 papers reporting on new databases and 85 updates from resources previously published …
FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomics
Spatial transcriptomics (ST) technologies have advanced to enable transcriptome-wide
gene expression analysis at submicron resolution over large areas. However, analysis of …
gene expression analysis at submicron resolution over large areas. However, analysis of …
A single-cell transcriptome atlas reveals the trajectory of early cell fate transition during callus induction in Arabidopsis
R Yin, R Chen, K **a, X Xu - Plant Communications, 2024 - cell.com
The acquisition of pluripotent callus from somatic cells plays an important role in plant
development studies and crop genetic improvement. This developmental process …
development studies and crop genetic improvement. This developmental process …
A spatiotemporal atlas of cholestatic injury and repair in mice
Cholestatic liver injuries, characterized by regional damage around the bile ductular region,
lack curative therapies and cause considerable mortality. Here we generated a high …
lack curative therapies and cause considerable mortality. Here we generated a high …
SpatialRef: a reference of spatial omics with known spot annotation
T Cui, YY Li, BL Li, H Zhang, TT Yu… - Nucleic Acids …, 2025 - academic.oup.com
Spatial omics technologies have enabled the creation of intricate spatial maps that capture
molecular features and tissue morphology, providing valuable insights into the spatial …
molecular features and tissue morphology, providing valuable insights into the spatial …
Lamination-based organoid spatially resolved transcriptomics technique for primary lung and liver organoid characterization
Spatial-transcriptomics technologies have demonstrated exceptional performance in
characterizing brain and visceral organ tissues, as well as brain and retinal organoids …
characterizing brain and visceral organ tissues, as well as brain and retinal organoids …