Streamlining spatial omics data analysis with Pysodb

S Lin, F Zhao, Z Wu, J Yao, Y Zhao, Z Yuan - Nature Protocols, 2024 - nature.com
Advances in spatial omics technologies have improved the understanding of cellular
organization in tissues, leading to the generation of complex and heterogeneous data and …

STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization

Z Xu, W Wang, T Yang, L Li, X Ma, J Chen… - Nucleic acids …, 2024 - academic.oup.com
Recent technological developments in spatial transcriptomics allow researchers to measure
gene expression of cells and their spatial locations at the single-cell level, generating …

Harnessing computational spatial omics to explore the spatial biology intricacies

Z Yuan, J Yao - Seminars in Cancer Biology, 2023 - Elsevier
Spatially resolved transcriptomics (SRT) has unlocked new dimensions in our
understanding of intricate tissue architectures. However, this rapidly expanding field …

SpatialData: an open and universal data framework for spatial omics

L Marconato, G Palla, KA Yamauchi, I Virshup… - Nature …, 2024 - nature.com
Spatially resolved omics technologies are transforming our understanding of biological
tissues. However, the handling of uni-and multimodal spatial omics datasets remains a …

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 …

MENDER: fast and scalable tissue structure identification in spatial omics data

Z Yuan - Nature Communications, 2024 - nature.com
Tissue structure identification is a crucial task in spatial omics data analysis, for which
increasingly complex models, such as Graph Neural Networks and Bayesian networks, are …

Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics

Z Li, X Chen, X Zhang, R Jiang, S Chen - Genome Research, 2023 - genome.cshlp.org
Rapid advances in spatial transcriptomics (ST) have revolutionized the interrogation of
spatial heterogeneity and increase the demand for comprehensive methods to effectively …

STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data

X Li, C Xiao, J Qi, W Xue, X Xu, Z Mu… - Nucleic acids …, 2023 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) provides insights into gene expression
heterogeneities in diverse cell types underlying homeostasis, development and pathological …

A global database for modeling tumor-immune cell communication

Y Xie, W Zhou, J Shi, M Xu, Z Lin, D Li, J Li, S Cheng… - Scientific Data, 2023 - nature.com
Communications between tumor cells and surrounding immune cells help shape the tumor
immunity continuum. Recent breakthroughs in high-throughput technologies as well as …

SCAR: single-cell and Spatially-resolved Cancer Resources

Y Deng, P Chen, J Xiao, M Li, J Shen… - Nucleic Acids …, 2024 - academic.oup.com
Advances in sequencing and imaging technologies offer a unique opportunity to unravel cell
heterogeneity and develop new immunotherapy strategies for cancer research. There is an …