SiFT: uncovering hidden biological processes by probabilistic filtering of single-cell data

Zoe Piran, Mor Nitzan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Cellular populations simultaneously encode multiple biological attributes, including spatial configuration, temporal trajectories, and cell-cell interactions. Some of these signals may be overshadowed by others and harder to recover, despite the great progress made to computationally reconstruct biological processes from single-cell data. To address this, we present SiFT, a kernel-based projection method for filtering biological signals in single-cell data, thus uncovering underlying biological processes. SiFT applies to a wide range of tasks, from the removal of unwanted variation in the data to revealing hidden biological structures. We demonstrate how SiFT enhances the liver circadian signal by filtering spatial zonation, recovers regenerative cell subpopulations in spatially-resolved liver data, and exposes COVID-19 disease-related cells, pathways, and dynamics by filtering healthy reference signals. SiFT performs the correction at the gene expression level, can scale to large datasets, and compares favorably to state-of-the-art methods.

Original languageAmerican English
Article number760
JournalNature Communications
Volume15
Issue number1
DOIs
StatePublished - 26 Jan 2024

Bibliographical note

Publisher Copyright:
© 2024, The Author(s).

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