Using clusterProfiler to characterize multiomics data

S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang… - Nature protocols, 2024 - nature.com
With the advent of multiomics, software capable of multidimensional enrichment analysis
has become increasingly crucial for uncovering gene set variations in biological processes …

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 …

BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis

V Singhal, N Chou, J Lee, Y Yue, J Liu, WK Chock… - Nature Genetics, 2024 - nature.com
Spatial omics data are clustered to define both cell types and tissue domains. We present
Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an …

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 …

Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of view

J Zhu, K Pang, B Hu, R He, N Wang, Z Jiang, P Ji… - Nature Genetics, 2024 - nature.com
Spatial transcriptomic techniques offer unprecedented insights into the molecular
organization of complex tissues. However, integrating cost-effectiveness, high throughput, a …

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 …

Cross-species single-cell spatial transcriptomic atlases of the cerebellar cortex

S Hao, X Zhu, Z Huang, Q Yang, H Liu, Y Wu, Y Zhan… - Science, 2024 - science.org
The molecular and cellular organization of the primate cerebellum remains poorly
characterized. We obtained single-cell spatial transcriptomic atlases of macaque, marmoset …

Repurposing large-format microarrays for scalable spatial transcriptomics

D Cipurko, T Ueda, L Mei, N Chevrier - Nature Methods, 2024 - nature.com
Spatiomolecular analyses are key to study tissue functions and malfunctions. However, we
lack profiling tools for spatial transcriptomics that are easy to adopt, low cost and scalable in …

Lost in space: what single-cell RNA sequencing cannot tell you

K Adema, MA Schon, MD Nodine, W Kohlen - Trends in Plant Science, 2024 - cell.com
Plant scientists are rapidly integrating single-cell RNA sequencing (scRNA-seq) into their
workflows. Maximizing the potential of scRNA-seq requires a proper understanding of the …

Axo-axonic synaptic input drives homeostatic plasticity by tuning the axon initial segment structurally and functionally

R Zhao, B Ren, Y Xiao, J Tian, Y Zou, J Wei, Y Qi… - Science …, 2024 - science.org
Homeostatic plasticity maintains the stability of functional brain networks. The axon initial
segment (AIS), where action potentials start, undergoes dynamic adjustment to exert …