Integrating single-cell transcriptomics with cellular phenotypes: cell morphology, Ca2+ imaging and electrophysiology

J Camunas-Soler - Biophysical Reviews, 2024 - Springer
I review recent technological advancements in coupling single-cell transcriptomics with
cellular phenotypes including morphology, calcium signaling, and electrophysiology. Single …

A comparative analysis of imaging-based spatial transcriptomics platforms

DP Cook, KB Jensen, K Wise, MJ Roach, FS Dezem… - bioRxiv, 2023 - biorxiv.org
Spatial transcriptomics is a rapidly evolving field, overwhelmed by a multitude of
technologies. This study aims to offer a comparative analysis of datasets generated from …

Integrating spatially-resolved transcriptomics data across tissues and individuals: challenges and opportunities

B Guo, W Ling, SH Kwon, P Panwar, S Ghazanfar… - ArXiv, 2024 - pmc.ncbi.nlm.nih.gov
Advances in spatially-resolved transcriptomics (SRT) technologies have propelled the
development of new computational analysis methods to unlock biological insights. As the …

[HTML][HTML] Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem

JG Chen, JC Chávez-Fuentes, M O'Brien, J Xu, E Ruiz… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Emerging spatial omics technologies continue to advance the molecular mapping of tissue
architecture and the investigation of gene regulation and cellular crosstalk, which in turn …

ST-GEARS: Advancing 3D downstream research through accurate spatial information recovery

T Xia, L Hu, L Zuo, L Cao, Y Zhang, M Xu, Q Lu… - Nature …, 2024 - nature.com
Abstract Three-dimensional Spatial Transcriptomics has revolutionized our understanding of
tissue regionalization, organogenesis, and development. However, existing approaches …

[HTML][HTML] Sex matters: the MouseX DW-ALLEN Atlas for mice diffusion-weighted MR imaging

P Martínez-Tazo, A Santos, MK Selim, E Espinos-Soler… - NeuroImage, 2024 - Elsevier
Overcoming sex bias in preclinical research requires not only including animals of both
sexes in the experiments, but also developing proper tools to handle such data. Recent work …

DeST-OT: Alignment of Spatiotemporal Transcriptomics Data

P Halmos, X Liu, J Gold, F Chen, L Ding… - … on Research in …, 2024 - Springer
Spatially resolved transcriptomics (SRT) measures mRNA transcripts at thousands of
locations within a tissue slice, revealing spatial variations in gene expression as well as the …

[HTML][HTML] ATAT: Automated Tissue Alignment and Traversal in Spatial Transcriptomics with Self-Supervised Learning

S Song, E Mohsin, R Zhang, A Kuznetsov, L Shen… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Spatial transcriptomics (ST) has enhanced RNA analysis in tissue biopsies, but interpreting
these data is challenging without expert input. We present Automated Tissue Alignment and …