A relay velocity model infers cell-dependent RNA velocity

S Li, P Zhang, W Chen, L Ye, KW Brannan, NT Le… - Nature …, 2024 - nature.com
RNA velocity provides an approach for inferring cellular state transitions from single-cell
RNA sequencing (scRNA-seq) data. Conventional RNA velocity models infer universal …

UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference

M Gao, C Qiao, Y Huang - Nature Communications, 2022 - nature.com
The recent breakthrough of single-cell RNA velocity methods brings attractive promises to
reveal directed trajectory on cell differentiation, states transition and response to …

Generalizing RNA velocity to transient cell states through dynamical modeling

V Bergen, M Lange, S Peidli, FA Wolf, FJ Theis - Nature biotechnology, 2020 - nature.com
RNA velocity has opened up new ways of studying cellular differentiation in single-cell RNA-
sequencing data. It describes the rate of gene expression change for an individual gene at a …

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

A Gayoso, P Weiler, M Lotfollahi, D Klein, J Hong… - Nature …, 2024 - nature.com
RNA velocity has been rapidly adopted to guide interpretation of transcriptional dynamics in
snapshot single-cell data; however, current approaches for estimating RNA velocity lack …

Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation

M Barile, I Imaz-Rosshandler, I Inzani, S Ghazanfar… - Genome biology, 2021 - Springer
Background Single-cell technologies are transforming biomedical research, including the
recent demonstration that unspliced pre-mRNA present in single-cell RNA-Seq permits …

DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations

Z Chen, WC King, A Hwang, M Gerstein, J Zhang - Science advances, 2022 - science.org
Recent advances in single-cell sequencing technologies have provided unprecedented
opportunities to measure the gene expression profile and RNA velocity of individual cells …

[PDF][PDF] RNA velocity: molecular kinetics from single-cell RNA-Seq

V Svensson, L Pachter - Molecular cell, 2018 - cell.com
RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq Page 1 Molecular Cell Spotlight
RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq Valentine Svensson1,* and Lior …

PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes

K Wang, L Hou, X Wang, X Zhai, Z Lu, Z Zi… - Nature …, 2023 - nature.com
Single-cell RNA sequencing (scRNA-seq) is a powerful approach for studying cellular
differentiation, but accurately tracking cell fate transitions can be challenging, especially in …

Protein velocity and acceleration from single-cell multiomics experiments

G Gorin, V Svensson, L Pachter - Genome biology, 2020 - Springer
The simultaneous quantification of protein and RNA makes possible the inference of past,
present, and future cell states from single experimental snapshots. To enable such temporal …

[PDF][PDF] Mapping transcriptomic vector fields of single cells

X Qiu, Y Zhang, JD Martin-Rufino, C Weng… - Cell, 2022 - cell.com
Summary Single-cell (sc) RNA-seq, together with RNA velocity and metabolic labeling,
reveals cellular states and transitions at unprecedented resolution. Fully exploiting these …