Article

Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors

2022-10-21

Abstract excerpt

Single-cell expression dynamics from differentiation trajectories or RNA velocity have the potential to reveal causal links between transcription factors (TFs) and their target genes in gene regulatory networks (GRNs). However, existing methods either neglect these expression dynamics or require cells to be ordered along a linear pseudotemporal axis, which is incompatible with branching trajectories. We introduce...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 50900717-4135-5ea3-a4d3-68e38f4fb6a4
DOI: 10.1101/2022.10.18.512766

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factorsDOI 10.1101/2022.10.18.512766Read

Experimental Time Points Guided Transcriptomic Velocity InferenceSemantic proximity Read

Optimal transport reveals dynamic gene regulatory networks via gene velocity estimationSemantic proximity Read

Model-based inference of RNA velocity modules improves cell fate predictionSemantic proximity Read

ArchVelo: Archetypal Velocity Modeling for Single-cell Multi-omic TrajectoriesSemantic proximity Read

TIVelo: RNA velocity estimation leveraging cluster-level trajectory inferenceSemantic proximity Read

Integrating temporal single-cell gene expression modalities for trajectory inference and disease predictionSemantic proximity Read

VAPOR: A variational autoencoder with transport operators to disentangle cellular gene expression dynamics of co-occurring biological processes in time and spaceSemantic proximity Read

Tracing co-regulatory network dynamics in noisy, single-cell transcriptome trajectoriesSemantic proximity Read

Characterization of cell-fate decision landscapes by estimating transcription factor dynamicsSemantic proximity Read

StaVia: Spatially and temporally aware cartography with higher order random walks for cell atlasesSemantic proximity Read

Identifying transcription factors driving cell differentiationSemantic proximity Read

CycleGRN: Inferring Gene Regulatory Networks from Cyclic Flow Dynamics in Single-Cell RNA-seqSemantic proximity Read