Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA

J Hu, K Coleman, D Zhang, EB Lee, H Kadara, L Wang… - Cell systems, 2023 - cell.com
Cell populations in the tumor microenvironment (TME), including their abundance,
composition, and spatial location, are critical determinants of patient response to therapy …

Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing

J Cao, Z Zheng, D Sun, X Chen, R Cheng, T Lv… - Nature …, 2024 - nature.com
Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA
detection. Here we report a dendrimeric DNA coordinate barcoding design for spatial RNA …

Mapping human tissues with highly multiplexed RNA in situ hybridization

K Kalhor, CJ Chen, HS Lee, M Cai, M Nafisi… - Nature …, 2024 - nature.com
In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell
interactions. There has been a surge of multiplexed RNA in situ mapping techniques but …

Explainable multiview framework for dissecting spatial relationships from highly multiplexed data

J Tanevski, ROR Flores, A Gabor, D Schapiro… - Genome biology, 2022 - Springer
The advancement of highly multiplexed spatial technologies requires scalable methods that
can leverage spatial information. We present MISTy, a flexible, scalable, and explainable …

Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing

J Liu, V Tran, VNP Vemuri, A Byrne… - Life science …, 2023 - life-science-alliance.org
Spatial transcriptomics extends single-cell RNA sequencing (scRNA-seq) by providing
spatial context for cell type identification and analysis. Imaging-based spatial technologies …

standR: spatial transcriptomic analysis for GeoMx DSP data

N Liu, DD Bhuva, A Mohamed, M Bokelund… - Nucleic Acids …, 2024 - academic.oup.com
To gain a better understanding of the complexity of gene expression in normal and diseased
tissues it is important to account for the spatial context and identity of cells in situ. State-of …

Navigating bottlenecks and trade-offs in genomic data analysis

B Berger, YW Yu - Nature Reviews Genetics, 2023 - nature.com
Genome sequencing and analysis allow researchers to decode the functional information
hidden in DNA sequences as well as to study cell to cell variation within a cell population …

CROST: a comprehensive repository of spatial transcriptomics

G Wang, S Wu, Z Xiong, H Qu, X Fang… - Nucleic Acids …, 2024 - academic.oup.com
The development of spatial transcriptome sequencing technology has revolutionized our
comprehension of complex tissues and propelled life and health sciences into an era of …

A comprehensive comparison on cell-type composition inference for spatial transcriptomics data

J Chen, W Liu, T Luo, Z Yu, M Jiang… - Briefings in …, 2022 - academic.oup.com
Spatial transcriptomics (ST) technologies allow researchers to examine transcriptional
profiles along with maintained positional information. Such spatially resolved transcriptional …

Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics

Z Li, X Chen, X Zhang, R Jiang, S Chen - Genome Research, 2023 - genome.cshlp.org
Rapid advances in spatial transcriptomics (ST) have revolutionized the interrogation of
spatial heterogeneity and increase the demand for comprehensive methods to effectively …