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 …

Navigating the landscapes of spatial transcriptomics: How computational methods guide the way

R Li, X Chen, X Yang - Wiley Interdisciplinary Reviews: RNA, 2024 - Wiley Online Library
Spatially resolved transcriptomics has been dramatically transforming biological and
medical research in various fields. It enables transcriptome profiling at single‐cell, multi …

Multi-slice spatial transcriptome domain analysis with SpaDo

B Duan, S Chen, X Cheng, Q Liu - Genome Biology, 2024 - Springer
With the rapid advancements in spatial transcriptome sequencing, multiple tissue slices are
now available, enabling the integration and interpretation of spatial cellular landscapes …

Spatial omics advances for in situ RNA biology

J Ren, S Luo, H Shi, X Wang - Molecular Cell, 2024 - cell.com
Spatial regulation of RNA plays a critical role in gene expression regulation and cellular
function. Understanding spatially resolved RNA dynamics and translation is vital for bringing …

Cross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections

KM Stouffer, A Trouvé, L Younes, M Kunst, L Ng… - Nature …, 2024 - nature.com
This paper explicates a solution to building correspondences between molecular-scale
transcriptomics and tissue-scale atlases. This problem arises in atlas construction and cross …

Dissecting tumor microenvironment from spatially resolved transcriptomics data by heterogeneous graph learning

C Zuo, J Xia, L Chen - Nature Communications, 2024 - nature.com
Spatially resolved transcriptomics (SRT) has enabled precise dissection of tumor-
microenvironment (TME) by analyzing its intracellular molecular networks and intercellular …

SANTO: a coarse-to-fine alignment and stitching method for spatial omics

H Li, Y Lin, W He, W Han, X Xu, C Xu, E Gao… - Nature …, 2024 - nature.com
With the flourishing of spatial omics technologies, alignment and stitching of slices becomes
indispensable to decipher a holistic view of 3D molecular profile. However, existing …

ST-GEARS: Advancing 3D downstream research through accurate spatial information recovery

T Xia, L Hu, L Zuo, L Cao, Y Zhang, M Xu, Q Lu… - Nature …, 2024 - nature.com
Abstract Three-dimensional Spatial Transcriptomics has revolutionized our understanding of
tissue regionalization, organogenesis, and development. However, existing approaches …

A practical guide to spatial transcriptomics

L Valihrach, D Zucha, P Abaffy, M Kubista - Molecular Aspects of Medicine, 2024 - Elsevier
Spatial transcriptomics is revolutionizing modern biology, offering researchers an
unprecedented ability to unravel intricate gene expression patterns within tissues. From …

Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro

Z Chang, Y Xu, X Dong, Y Gao, C Wang - Bioinformatics, 2024 - academic.oup.com
Motivation The burgeoning generation of single-cell or spatial multiomic data allows for the
characterization of gene regulation networks (GRNs) at an unprecedented resolution …