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Modeling latent flows on single-cell data using the Hodge decomposition

https://doi.org/10.1101/592089
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/eji.201646347openalex-snapshot
Computational methods for trajectory inference from single‐cell transcriptomics
inferredcites →https://doi.org/10.1007/s10107-010-0419-xopenalex-snapshot
Statistical ranking and combinatorial Hodge theory
inferredcites →https://doi.org/10.1016/j.acha.2005.07.004openalex-snapshot
Diffusion maps, spectral clustering and reaction coordinates of dynamical systems
inferredcites →https://doi.org/10.1016/j.acha.2006.04.006openalex-snapshot
Diffusion maps
inferredcites →https://doi.org/10.1016/j.cell.2014.04.005openalex-snapshot
Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development
inferredcites →https://doi.org/10.1016/j.cell.2019.01.006openalex-snapshot
Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming
inferredcites →https://doi.org/10.1016/j.cell.2019.02.026openalex-snapshot
Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming
inferredcites →https://doi.org/10.1016/j.cub.2012.03.045openalex-snapshot
Bistability, Bifurcations, and Waddington's Epigenetic Landscape
inferredcites →https://doi.org/10.1016/j.stem.2018.04.014openalex-snapshot
Single-Cell Transcriptomics Meets Lineage Tracing
inferredcites →https://doi.org/10.1016/j.ymeth.2015.06.021openalex-snapshot
Computational assignment of cell-cycle stage from single-cell transcriptome data
inferredcites →https://doi.org/10.1038/nature18323openalex-snapshot
Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq
inferredcites →https://doi.org/10.1038/nbt.2859openalex-snapshot
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
inferredcites →https://doi.org/10.1038/nbt.3569openalex-snapshot
Wishbone identifies bifurcating developmental trajectories from single-cell data
inferredcites →https://doi.org/10.1038/nmeth.3549openalex-snapshot
Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments
inferredcites →https://doi.org/10.1038/nmeth.3971openalex-snapshot
Diffusion pseudotime robustly reconstructs lineage branching
inferredcites →https://doi.org/10.1038/s41467-017-00039-zopenalex-snapshot
Reconstructing cell cycle pseudo time-series via single-cell transcriptome data
inferredcites →https://doi.org/10.1038/s41556-018-0248-3openalex-snapshot
A chromatin integration labelling method enables epigenomic profiling with lower input
inferredcites →https://doi.org/10.1038/s41587-019-0071-9openalex-snapshot
A comparison of single-cell trajectory inference methods
inferredcites →https://doi.org/10.1101/120378openalex-snapshot
Visualizing Structure and Transitions for Biological Data Exploration
inferredcites →https://doi.org/10.1145/1273496.1273604openalex-snapshot
A kernel-based causal learning algorithm
inferredcites →https://doi.org/10.1186/gb-2010-11-10-r106openalex-snapshot
Differential expression analysis for sequence count data
inferredcites →https://doi.org/10.1186/s12859-016-1109-3openalex-snapshot
SCOUP: a probabilistic model based on the Ornstein–Uhlenbeck process to analyze single-cell expression data during differentiation
inferredcites →https://doi.org/10.1214/09-aos685openalex-snapshot
Estimating high-dimensional intervention effects from observational data
inferredcites →https://doi.org/10.1214/11-aos878openalex-snapshot
The solution path of the generalized lasso
inferredcites →https://doi.org/10.5694/j.1326-5377.1958.tb86500.xopenalex-snapshot
The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/advs.202308879openalex-snapshot
Quantifying Landscape‐Flux via Single‐Cell Transcriptomics Uncovers the Underlying Mechanism of Cell Cycle
inferred← citeshttps://doi.org/10.1016/j.cell.2021.12.045openalex-snapshot
Mapping transcriptomic vector fields of single cells
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00132openalex-snapshot
Hodge Decomposition of Single-Cell RNA Velocity
inferred← citeshttps://doi.org/10.1029/2024jd040830openalex-snapshot
An Objective Detection of Separation Scenario in Tropical Cyclone Trajectories Based On Ensemble Weather Forecast Data
inferred← citeshttps://doi.org/10.1038/s41592-025-02870-5openalex-snapshot
PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories
inferred← citeshttps://doi.org/10.1101/2023.09.24.559170openalex-snapshot
Graph-Dynamo: Learning stochastic cellular state transition dynamics from single cell data
inferred← citeshttps://doi.org/10.1101/2024.10.01.613179openalex-snapshot
PHLOWER - Single cell trajectory analysis using Hodge Decomposition
inferred← citeshttps://doi.org/10.1101/696724openalex-snapshot
Mapping Transcriptomic Vector Fields of Single Cells
inferred← citeshttps://doi.org/10.1177/23998083231180608openalex-snapshot
Identifying sinks and sources of human flows: A new approach to characterizing urban structures
inferred← citeshttps://doi.org/10.1587/nolta.14.92openalex-snapshot
V-Mapper: topological data analysis for high-dimensional data with velocity
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