Deep learning in spatially resolved transcriptfomics: a comprehensive technical view

R Zahedi, R Ghamsari, A Argha… - Briefings in …, 2024 - academic.oup.com
Spatially resolved transcriptomics (SRT) is a pioneering method for simultaneously studying
morphological contexts and gene expression at single-cell precision. Data emerging from …

Deep learning in spatially resolved transcriptomics: A comprehensive technical view

RZ Nasab, MRE Ghamsari, A Argha… - arXiv preprint arXiv …, 2022 - arxiv.org
Spatially resolved transcriptomics (SRT) has evolved rapidly through various technologies,
enabling scientists to investigate both morphological contexts and gene expression profiling …

[HTML][HTML] Statistical and machine learning methods for spatially resolved transcriptomics with histology

J Hu, A Schroeder, K Coleman, C Chen… - Computational and …, 2021 - Elsevier
Recent developments in spatially resolved transcriptomics (SRT) technologies have
enabled scientists to get an integrated understanding of cells in their morphological context …

Mitigating autocorrelation during spatially resolved transcriptomics data analysis

K Maher, M Wu, Y Zhou, J Huang, Q Zhang, X Wang - bioRxiv, 2023 - biorxiv.org
Several computational methods have recently been developed for characterizing molecular
tissue regions in spatially resolved transcriptomics (SRT) data. However, each method …

[HTML][HTML] Recent advances in spatially resolved transcriptomics: challenges and opportunities

J Lee, M Yoo, J Choi - BMB reports, 2022 - ncbi.nlm.nih.gov
Single-cell RNA sequencing (scRNA-seq) has greatly advanced our understanding of
cellular heterogeneity by profiling individual cell transcriptomes. However, cell dissociation …

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 …

Deep learning in spatial transcriptomics: Learning from the next next-generation sequencing

AA Heydari, SS Sindi - Biophysics Reviews, 2023 - pubs.aip.org
Spatial transcriptomics (ST) technologies are rapidly becoming the extension of single-cell
RNA sequencing (scRNAseq), holding the potential of profiling gene expression at a single …

Integrating image and molecular profiles for spatial transcriptomics analysis

X Jiang, S Wang, L Guo, Z Wen, L Jia, L Xu, G Xiao… - bioRxiv, 2023 - biorxiv.org
The spatially resolved transcriptomics (SRT) field has revolutionized our ability to
comprehensively leverage image and molecular profiles to elucidate spatial organization of …

Bioinformatics approach to spatially resolved transcriptomics

I Krešimir Lukić - Emerging Topics in Life Sciences, 2021 - portlandpress.com
Spatially resolved transcriptomics encompasses a growing number of methods developed to
enable gene expression profiling of individual cells within a tissue. Different technologies …

[HTML][HTML] Reconstructing Spatial Transcriptomics at the Single-cell Resolution with BayesDeep

X Jiang, L Dong, S Wang, Z Wen, M Chen, L Xu, G Xiao… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Spatially resolved transcriptomics (SRT) techniques have revolutionized the characterization
of molecular profiles while preserving spatial and morphological context. However, most …