Introducing single cell stereo-sequencing technology to transform the plant transcriptome landscape

G Bawa, Z Liu, X Yu, LSP Tran, X Sun - Trends in Plant Science, 2024 - cell.com
Single cell RNA-sequencing (scRNA-seq) advancements have helped detect transcriptional
heterogeneities in biological samples. However, scRNA-seq cannot currently provide high …

STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization

Z Xu, W Wang, T Yang, L Li, X Ma, J Chen… - Nucleic acids …, 2024 - academic.oup.com
Recent technological developments in spatial transcriptomics allow researchers to measure
gene expression of cells and their spatial locations at the single-cell level, generating …

Future avenues in Drosophila mushroom body research

ICW Chan, N Chen, J Hernandez, H Meltzer… - Learning & …, 2024 - learnmem.cshlp.org
How does the brain translate sensory information into complex behaviors? With relatively
small neuronal numbers, readable behavioral outputs, and an unparalleled genetic toolkit …

3D reconstruction of a gastrulating human embryo

Z Xiao, L Cui, Y Yuan, N He, X Xie, S Lin, X Yang… - Cell, 2024 - cell.com
Progress in understanding early human development has been impeded by the scarcity of
reference datasets from natural embryos, particularly those with spatial information during …

CellRank 2: unified fate mapping in multiview single-cell data

P Weiler, M Lange, M Klein, D Pe'er, F Theis - Nature Methods, 2024 - nature.com
Single-cell RNA sequencing allows us to model cellular state dynamics and fate decisions
using expression similarity or RNA velocity to reconstruct state-change trajectories; however …

EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics

T Lv, Y Zhang, M Li, Q Kang, S Fang, Y Zhang… - …, 2024 - academic.oup.com
Background The emergence of high-resolved spatial transcriptomics (ST) has facilitated the
research of novel methods to investigate biological development, organism growth, and …

High-density generation of spatial transcriptomics with STAGE

S Li, K Gai, K Dong, Y Zhang… - Nucleic Acids Research, 2024 - academic.oup.com
Spatial transcriptome technologies have enabled the measurement of gene expression
while maintaining spatial location information for deciphering the spatial heterogeneity of …

CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics

Y Zhao, C Kohl, D Rosebrock, Q Hu, Y Hu… - Nucleic Acids …, 2024 - academic.oup.com
A fundamental analysis task for single-cell transcriptomics data is clustering with subsequent
visualization of cell clusters. The genes responsible for the clustering are only inferred in a …

[HTML][HTML] Challenges and Opportunities for the Clinical Translation of Spatial Transcriptomics Technologies

KD Smith, DK Prince, JW MacDonald… - Glomerular …, 2024 - karger.com
Background: The first spatially resolved transcriptomics platforms, GeoMx (Nanostring) and
Visium (10x Genomics) were launched in 2019 and were recognized as the method of the …

SCAN: Spatiotemporal Cloud Atlas for Neural cells

Y Deng, Y Lu, M Li, J Shen, S Qin… - Nucleic Acids …, 2024 - academic.oup.com
The nervous system is one of the most complicated and enigmatic systems within the animal
kingdom. Recently, the emergence and development of spatial transcriptomics (ST) and …