The expanding vistas of spatial transcriptomics

L Tian, F Chen, EZ Macosko - Nature Biotechnology, 2023 - nature.com
The formation and maintenance of tissue integrity requires complex, coordinated activities
by thousands of genes and their encoded products. Until recently, transcript levels could …

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

SK Longo, MG Guo, AL Ji, PA Khavari - Nature Reviews Genetics, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …

[HTML][HTML] Mapping transcriptomic vector fields of single cells

X Qiu, Y Zhang, JD Martin-Rufino, C Weng… - Cell, 2022 - cell.com
Summary Single-cell (sc) RNA-seq, together with RNA velocity and metabolic labeling,
reveals cellular states and transitions at unprecedented resolution. Fully exploiting these …

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 …

[HTML][HTML] Machine learning for perturbational single-cell omics

Y Ji, M Lotfollahi, FA Wolf, FJ Theis - Cell Systems, 2021 - cell.com
Cell biology is fundamentally limited in its ability to collect complete data on cellular
phenotypes and the wide range of responses to perturbation. Areas such as computer vision …

Modular, programmable RNA sensing using ADAR editing in living cells

KE Kaseniit, N Katz, NS Kolber, CC Call… - Nature …, 2023 - nature.com
With the increasing availability of single-cell transcriptomes, RNA signatures offer a
promising basis for targeting living cells. Molecular RNA sensors would enable the study of …

The role of osteopontin in microglia biology: current concepts and future perspectives

DD Rosmus, C Lange, F Ludwig, B Ajami, P Wieghofer - Biomedicines, 2022 - mdpi.com
The innate immune landscape of the central nervous system (CNS), including the brain and
the retina, consists of different myeloid cell populations with distinct tasks to fulfill. Whereas …

Spatial transcriptomics: recent developments and insights in respiratory research

WJ Wang, LX Chu, LY He, MJ Zhang, KT Dang… - Military Medical …, 2023 - Springer
The respiratory system's complex cellular heterogeneity presents unique challenges to
researchers in this field. Although bulk RNA sequencing and single-cell RNA sequencing …

Microfluidics-based single cell analysis: from transcriptomics to spatiotemporal multi-omics

J Cao, X Chen, S Huang, W Shi, Q Fan, Y Gong… - TrAC Trends in …, 2023 - Elsevier
Uncover cell composition, cellular spatial distribution, and cell-to-cell interactions in tissues
are significant for the understanding of physiological and pathological processes. Over the …

[HTML][HTML] Molecular recording: transcriptional data collection into the genome

SK Lear, SL Shipman - Current opinion in biotechnology, 2023 - Elsevier
Highlights•Molecular recorders capture transcriptional activity within the genome of
cells.•Transcriptional activity is recorded by linking a signal of interest to a DNA …