ArticleCell reports methods2022
Simulation-based inference of differentiation trajectories from RNA velocity fields.
Article in Cell reports methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Sensitivity analysis of cell fate trajectories from single-cell transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Data-intensive immune network modelling for One Health.Briefings in bioinformatics · 2026Review
- Histone modifications across cancers: mechanisms, therapy and clinical translation.Molecular cancer · 2026Review
- Predicting trajectories of illness using RNA velocity of whole blood.Nature communications · 2026Observational
- Article
- Fundamental errors in RNA velocity arising from the omission of cell growth.bioRxiv : the preprint server for biology · 2025Article
- Paradigms, innovations, and biological applications of RNA velocity: a comprehensive review.Briefings in bioinformatics · 2025Review
- The endogenous antigen-specific CD8Immunity · 2025Article
- Exploratory trajectory inference reveals convergent lineages for CD8 T cells in chronic LCMV infection.PloS one · 2025Article
- Population-Level Cell Trajectory Inference Based on Gaussian Distributions.Biomolecules · 2024Article
- Spatial transition tensor of single cells.Nature methods · 2024Article
- Hodge Decomposition of Single-Cell RNA Velocity.Journal of chemical information and modeling · 2024Article
- Hierarchal single-cell lineage tracing reveals differential fate commitment of CD8 T-cell clones in response to acute infection.bioRxiv : the preprint server for biology · 2024Article
- Variation and evolution analysis of SARS-CoV-2 using self-game sequence optimization.Frontiers in microbiology · 2024Article
- Inferring single-cell transcriptomic dynamics with structured latent gene expression dynamics.Cell reports methods · 2023Article
- A robust and accurate single-cell data trajectory inference method using ensemble pseudotime.BMC bioinformatics · 2023Article
- RNA velocity unraveled.PLoS computational biology · 2022Article
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5 authors.
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Abstract
We report Cytopath, a method for trajectory inference that takes advantage of transcriptional activity information from the RNA velocity of single cells to perform trajectory inference. Cytopath performs this task by defining a Markov chain model, simulating an ensemble of possible differentiation trajectories, and constructing a consensus trajectory. We show that Cytopath can recapitulate the topological and molecular characteristics of the differentiation process under study. In our analysis, we include differentiation trajectories with varying bifurcated, circular, convergent, and mixed topologies studied in single-snapshot as well as time-series single-cell RNA sequencing experiments. We demonstrate the capability to reconstruct differentiation trajectories, assess the association of RNA velocity-based pseudotime with actually elapsed process time, and identify drawbacks in current state-of-the art trajectory inference approaches.
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