A practical guide to spatial transcriptomics

L Valihrach, D Zucha, P Abaffy, M Kubista - Molecular Aspects of Medicine, 2024 - Elsevier
Spatial transcriptomics is revolutionizing modern biology, offering researchers an
unprecedented ability to unravel intricate gene expression patterns within tissues. From …

Complete spatially resolved gene expression is not necessary for identifying spatial domains

S Lin, Y Cui, F Zhao, Z Yang, J Song, J Yao, Y Zhao… - Cell Genomics, 2024 - cell.com
Spatially resolved transcriptomics (SRT) technologies have revolutionized the study of tissue
organization. We introduce a graph convolutional network with an attention and positive …

[PDF][PDF] Metric multidimensional scaling for large single-cell datasets using neural networks

S Canzar, VH Do, S Jelić, S Laue, D Matijević… - Algorithms for Molecular …, 2024 - Springer
Metric multidimensional scaling is one of the classical methods for embedding data into low-
dimensional Euclidean space. It creates the low-dimensional embedding by approximately …

Spatial Deconvolution of Cell Types and Cell States at Scale Utilizing TACIT

K Huynh, KM Tyc, BF Matuck, QT Easter, A Pratapa… - bioRxiv, 2024 - biorxiv.org
Identifying cell types and states remains a time-consuming and error-prone challenge for
spatial biology. While deep learning is increasingly used, it is difficult to generalize due to …

Spatial transcriptomics: a new frontier in cancer research

S Huang, L Ouyang, J Tang, K Qian, X Chen, Z Xu… - Clinical Cancer …, 2024 - Springer
Tumor research is a fundamental focus of medical science, yet the intrinsic heterogeneity
and complexity of tumors present challenges in understanding their biological mechanisms …

Spatial Deconvolution of Cell Types and Cell States at Scale Utilizing TACIT

J Liu, K Huynh, K Tyc, BF Matuck, Q Easter, A Pratapa… - 2024 - researchsquare.com
Identifying cell types and states remains a time-consuming, error-prone challenge for spatial
biology. While deep learning is increasingly used, it is difficult to generalize due to variability …

Library size can undermine accurate molecular and phenotypic subtyping in spatial transcriptomics data.

NC Fisher, SB Malla, N Jamieson, PD Dunne - bioRxiv, 2024 - biorxiv.org
In an era where transcriptomics-based subtyping, phenotyping and mechanistic
understanding is increasingly being driven by state-of-the-art spatially resolved …

Dimensionality Reduction and Denoising of Spatial Transcriptomics Data Using Dual-Channel Masked Graph Autoencoder

W Min, D Fang, J Chen, S Zhang - bioRxiv, 2024 - biorxiv.org
Recent advances in spatial transcriptomics (ST) technology allow researchers to
comprehensively measure gene expression patterns at the level of individual cells or even …

stDyer enables spatial domain clustering with dynamic graph embedding

K Xu, Y Xu, Z Wang, X Zhou, L Zhang - bioRxiv, 2024 - biorxiv.org
Spatial transcriptomics data provide insights into gene expression patterns within tissue
contexts, where identifying spatial domains with similar gene expression is crucial …