Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Medial Arterial Calcification: JACC State-of-the-Art Review

P Lanzer, FM Hannan, JD Lanzer, J Janzen… - Journal of the American …, 2021 - jacc.org
Medial arterial calcification (MAC) is a chronic systemic vascular disorder distinct from
atherosclerosis that is frequently but not always associated with diabetes mellitus, chronic …

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk

X Shao, C Li, H Yang, X Lu, J Liao, J Qian… - Nature …, 2022 - nature.com
Spatially resolved transcriptomics provides genetic information in space toward elucidation
of the spatial architecture in intact organs and the spatially resolved cell-cell …

Multiplex protein imaging in tumour biology

N de Souza, S Zhao, B Bodenmiller - Nature Reviews Cancer, 2024 - nature.com
Tissue imaging has become much more colourful in the past decade. Advances in both
experimental and analytical methods now make it possible to image protein markers in …

[HTML][HTML] Computational solutions for spatial transcriptomics

I Kleino, P Frolovaitė, T Suomi, LL Elo - Computational and structural …, 2022 - Elsevier
Transcriptome level expression data connected to the spatial organization of the cells and
molecules would allow a comprehensive understanding of how gene expression is …

Application of machine learning in spatial proteomics

M Mou, Z Pan, M Lu, H Sun, Y Wang… - Journal of Chemical …, 2022 - ACS Publications
Spatial proteomics is an interdisciplinary field that investigates the localization and dynamics
of proteins, and it has gained extensive attention in recent years, especially the subcellular …

Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

L Atta, K Clifton, M Anant, G Aihara, J Fan - Genome Biology, 2024 - Springer
Background Recent advances in imaging-based spatially resolved transcriptomics (im-SRT)
technologies now enable high-throughput profiling of targeted genes and their locations in …

Bayesian modeling of spatial molecular profiling data via Gaussian process

Q Li, M Zhang, Y **e, G **ao - Bioinformatics, 2021 - academic.oup.com
Motivation The location, timing and abundance of gene expression (both mRNA and
proteins) within a tissue define the molecular mechanisms of cell functions. Recent …

stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics

Z Fang, T Liu, R Zheng, M Yin, M Li - Briefings in Bioinformatics, 2024 - academic.oup.com
With the development of spatially resolved transcriptomics technologies, it is now possible to
explore the gene expression profiles of single cells while preserving their spatial context …