scPrisma infers, filters and enhances topological signals in single-cell data using spectral template matching

Jonathan Karin, Yonathan Bornfeld, Mor Nitzan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Single-cell RNA sequencing has been instrumental in uncovering cellular spatiotemporal context. This task is challenging as cells simultaneously encode multiple, potentially cross-interfering, biological signals. Here we propose scPrisma, a spectral computational method that uses topological priors to decouple, enhance and filter different classes of biological processes in single-cell data, such as periodic and linear signals. We apply scPrisma to the analysis of the cell cycle in HeLa cells, circadian rhythm and spatial zonation in liver lobules, diurnal cycle in Chlamydomonas and circadian rhythm in the suprachiasmatic nucleus in the brain. scPrisma can be used to distinguish mixed cellular populations by specific characteristics such as cell type and uncover regulatory networks and cell–cell interactions specific to predefined biological signals, such as the circadian rhythm. We show scPrisma’s flexibility in incorporating prior knowledge, inference of topologically informative genes and generalization to additional diverse templates and systems. scPrisma can be used as a stand-alone workflow for signal analysis and as a prior step for downstream single-cell analysis.

Original languageAmerican English
Pages (from-to)1645-1654
Number of pages10
JournalNature Biotechnology
Volume41
Issue number11
DOIs
StatePublished - Nov 2023

Bibliographical note

Publisher Copyright:
© 2023, The Author(s).

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