[HTML][HTML] Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding

R Shen, L Liu, Z Wu, Y Zhang, Z Yuan, J Guo… - Nature …, 2022 - nature.com
Spatially resolved transcriptomics provides the opportunity to investigate the gene
expression profiles and the spatial context of cells in naive state, but at low transcript …

[HTML][HTML] Identifying cell populations with scRNASeq

TS Andrews, M Hemberg - Molecular aspects of medicine, 2018 - Elsevier
Single-cell RNASeq (scRNASeq) has emerged as a powerful method for quantifying the
transcriptome of individual cells. However, the data from scRNASeq experiments is often …

[HTML][HTML] Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor–immune hubs

S He, Y Jin, A Nazaret, L Shi, X Chen… - Nature …, 2024 - nature.com
Spatially resolved gene expression profiling provides insight into tissue organization and
cell–cell crosstalk; however, sequencing-based spatial transcriptomics (ST) lacks single-cell …

Next-Generation Sequencing-Based Spatial Transcriptomics: A Perspective from Barcoding Chemistry

W Shi, J Zhang, S Huang, Q Fan, J Cao, J Zeng, L Wu… - JACS Au, 2024 - ACS Publications
Gene expression profiling of tissue cells with spatial context is in high demand to reveal cell
types, locations, and intercellular or molecular interactions for physiological and …

deCS: A Tool for Systematic Cell Type Annotations of Single-Cell RNA Sequencing Data Among Human Tissues

G Pei, F Yan, LM Simon, Y Dai, P Jia… - Genomics, Proteomics …, 2023 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex and
dynamic cellular mechanisms. However, cell type annotation remains a main challenge as it …

[HTML][HTML] From multitude to singularity: An up-to-date overview of scRNA-seq data generation and analysis

G Carangelo, A Magi, R Semeraro - Frontiers in Genetics, 2022 - frontiersin.org
Single cell RNA sequencing (scRNA-seq) is today a common and powerful technology in
biomedical research settings, allowing to profile the whole transcriptome of a very large …

Single-cell and spatial transcriptomics: Bridging current technologies with long-read sequencing

CU Yuan, FX Quah, M Hemberg - Molecular Aspects of Medicine, 2024 - Elsevier
Single-cell technologies have transformed biomedical research over the last decade,
opening up new possibilities for understanding cellular heterogeneity, both at the genomic …

[HTML][HTML] Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

A Deshpande, M Loth, DN Sidiropoulos, S Zhang… - Cell systems, 2023 - cell.com
Recent advances in spatial transcriptomics (STs) enable gene expression measurements
from a tissue sample while retaining its spatial context. This technology enables …

Integrative spatial single-cell analysis with graph-based feature learning

J Zhu, C Sabatti - Biorxiv, 2020 - biorxiv.org
We propose GLISS, a strategy to discover spatially-varying genes by integrating two data
sources:(1) spatial gene expression data such as image-based fluorescence in situ …

A single-cell-type transcriptomics map of human tissues

O Alam - Nature Genetics, 2021 - nature.com
As single-cell RNA sequencing (scRNA-seq) continues to reveal the functional
heterogeneity within tissue types, parallel advances in imaging and spatial analysis …