An introduction to spatial transcriptomics for biomedical research

CG Williams, HJ Lee, T Asatsuma, R Vento-Tormo… - Genome Medicine, 2022 - Springer
Single-cell transcriptomics (scRNA-seq) has become essential for biomedical research over
the past decade, particularly in developmental biology, cancer, immunology, and …

Museum of spatial transcriptomics

L Moses, L Pachter - Nature methods, 2022 - nature.com
The function of many biological systems, such as embryos, liver lobules, intestinal villi, and
tumors, depends on the spatial organization of their cells. In the past decade, high …

Screening cell–cell communication in spatial transcriptomics via collective optimal transport

Z Cang, Y Zhao, AA Almet, A Stabell, R Ramos… - Nature …, 2023 - nature.com
Spatial transcriptomic technologies and spatially annotated single-cell RNA sequencing
datasets provide unprecedented opportunities to dissect cell–cell communication (CCC) …

LNCcation: lncRNA localization and function

MC Bridges, AC Daulagala, A Kourtidis - Journal of Cell Biology, 2021 - rupress.org
Subcellular localization of RNAs has gained attention in recent years as a prevalent
phenomenon that influences numerous cellular processes. This is also evident for the large …

Intracellular mRNA transport and localized translation

S Das, M Vera, V Gandin, RH Singer… - Nature reviews Molecular …, 2021 - nature.com
Fine-tuning cellular physiology in response to intracellular and environmental cues requires
precise temporal and spatial control of gene expression. High-resolution imaging …

Transcriptional coupling of distant regulatory genes in living embryos

M Levo, J Raimundo, XY Bing, Z Sisco, PJ Batut… - Nature, 2022 - nature.com
The prevailing view of metazoan gene regulation is that individual genes are independently
regulated by their own dedicated sets of transcriptional enhancers. Past studies have …

Liquid–liquid phase separation in tumor biology

X Tong, R Tang, J Xu, W Wang, Y Zhao, X Yu… - Signal Transduction and …, 2022 - nature.com
Liquid–liquid phase separation (LLPS) is a novel principle for explaining the precise spatial
and temporal regulation in living cells. LLPS compartmentalizes proteins and nucleic acids …

Construction of a 3D whole organism spatial atlas by joint modelling of multiple slices with deep neural networks

G Wang, J Zhao, Y Yan, Y Wang, AR Wu… - Nature Machine …, 2023 - nature.com
Spatial transcriptomics (ST) technologies are revolutionizing the way to explore the spatial
architecture of tissues. Currently, ST data analysis is often restricted to a single two …

The maternal-to-zygotic transition revisited

NL Vastenhouw, WX Cao, HD Lipshitz - Development, 2019 - journals.biologists.com
The development of animal embryos is initially directed by maternal gene products. Then,
during the maternal-to-zygotic transition (MZT), developmental control is handed to the …

CircInteractome: a web tool for exploring circular RNAs and their interacting proteins and microRNAs

DB Dudekula, AC Panda, I Grammatikakis, S De… - RNA biology, 2016 - Taylor & Francis
Circular RNAs (circRNAs) are widely expressed in animal cells, but their biogenesis and
functions are poorly understood. CircRNAs have been shown to act as sponges for miRNAs …