Small molecule metabolites: discovery of biomarkers and therapeutic targets

S Qiu, Y Cai, H Yao, C Lin, Y Xie, S Tang… - Signal Transduction and …, 2023 - nature.com
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite
accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite …

Spatial multi-omics analyses of the tumor immune microenvironment

WC Hsieh, BR Budiarto, YF Wang, CY Lin… - Journal of Biomedical …, 2022 - Springer
In the past decade, single-cell technologies have revealed the heterogeneity of the tumor-
immune microenvironment at the genomic, transcriptomic, and proteomic levels and have …

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 …

Mass spectrometry imaging: the rise of spatially resolved single-cell omics

H Zhang, DG Delafield, L Li - nature methods, 2023 - nature.com
Increasing evidence suggests that the spatial distribution of biomolecules within cells is a
critical component in deciphering single-cell molecular heterogeneity. State-of-the-art single …

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk

X Shao, C Li, H Yang, X Lu, J Liao, J Qian… - Nature …, 2022 - nature.com
Spatially resolved transcriptomics provides genetic information in space toward elucidation
of the spatial architecture in intact organs and the spatially resolved cell-cell …

Single-cell lipidomics enabled by dual-polarity ionization and ion mobility-mass spectrometry imaging

H Zhang, Y Liu, L Fields, X Shi, P Huang, H Lu… - Nature …, 2023 - nature.com
Single-cell (SC) analysis provides unique insight into individual cell dynamics and cell-to-
cell heterogeneity. Here, we utilize trapped ion mobility separation coupled with dual …

High spatial resolution mass spectrometry imaging for spatial metabolomics: advances, challenges, and future perspectives

S Ma, Y Leng, X Li, Y Meng, Z Yin, W Hang - TrAC Trends in Analytical …, 2023 - Elsevier
Spatial metabolomics is an emerging field of omics research that has enabled localizing
small molecules in tissues and cells. Mass spectrometry imaging (MSI) technologies allow …

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 …

SOTIP is a versatile method for microenvironment modeling with spatial omics data

Z Yuan, Y Li, M Shi, F Yang, J Gao, J Yao… - Nature …, 2022 - nature.com
The rapidly developing spatial omics generated datasets with diverse scales and modalities.
However, most existing methods focus on modeling dynamics of single cells while ignore …

Rethinking the initial changes in subarachnoid haemorrhage: Focusing on real-time metabolism during early brain injury

Y Chen, I Galea, RL Macdonald, GKC Wong… - …, 2022 - thelancet.com
Over the last two decades, neurological researchers have uncovered many
pathophysiological mechanisms associated with subarachnoid haemorrhage (SAH), with …