ArticleNature methods2022
CellRank for directed single-cell fate mapping.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 462 papers.
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462 citing papers in PubMed.
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- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- PRISM-GEP: Viewing single-cell expression through the lens of topic modeling.Bioinformatics (Oxford, England) · 2026Article
- FlowMap: Geometry-Dynamics Consistent Embedding of RNA Velocity for Interpretable Cellular Trajectories.bioRxiv : the preprint server for biology · 2026Article
- Cell-level random splits leak group-owned answers in single-cell benchmarks.bioRxiv : the preprint server for biology · 2026Article
- Learning stochastic dynamics and cell-fate landscapes from single-cell snapshots via optimal transport.Science advances · 2026Article
- Explainable Artificial Intelligence and Gene-Network Analysis Prioritise a TREM2/LGALS3/GPNMB Scar-Associated Macrophage Programme in Human Liver Cirrhosis.International journal of molecular sciences · 2026Article
- Tumor-intrinsic IFNγ signaling and niche adaptation drive early colonization in ovarian cancer metastasis.Nature communications · 2026Article
- Multiomics analyses revealed the roles of the epithelial-mesenchymal transition and novel early candidate diagnostic biomarkers in neonatal necrotising enterocolitis.Clinical and translational medicine · 2026Article
- Stemness plasticity in hepatocellular carcinoma: spatial niches and therapeutic implications.Journal of liver cancer · 2026Article
- Gene-Chronos: parameter-efficient developmental time inference using a pretrained single-cell foundation model.Briefings in bioinformatics · 2026Article
- Single-cell transcriptomics of human brain disorders.Molecular psychiatry · 2026Review
- mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.Bioinformatics (Oxford, England) · 2026Article
- Article
- Tumor-induced dendritic cell deregulation perturbs T cell proliferation and predicts clinical outcome in acute lymphoblastic leukemia.Cell reports. Medicine · 2026Article
- Distinct postnatal trajectories of mouse dendritic epidermal T cells and Langerhans cells independent of microbiota.Science advances · 2026Article
- Uncovering smooth structures in single-cell data with neighbor embeddings guided by predictability-computability-stability.Patterns (New York, N.Y.) · 2026Article
- Malignant B-cell States Orchestrate Spatially Organized Immune Ecosystems in B-cell Lymphomas.Research square · 2026Article
402 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
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Abstract
Computational trajectory inference enables the reconstruction of cell state dynamics from single-cell RNA sequencing experiments. However, trajectory inference requires that the direction of a biological process is known, largely limiting its application to differentiating systems in normal development. Here, we present CellRank ( https://cellrank.org ) for single-cell fate mapping in diverse scenarios, including regeneration, reprogramming and disease, for which direction is unknown. Our approach combines the robustness of trajectory inference with directional information from RNA velocity, taking into account the gradual and stochastic nature of cellular fate decisions, as well as uncertainty in velocity vectors. On pancreas development data, CellRank automatically detects initial, intermediate and terminal populations, predicts fate potentials and visualizes continuous gene expression trends along individual lineages. Applied to lineage-traced cellular reprogramming data, predicted fate probabilities correctly recover reprogramming outcomes. CellRank also predicts a new dedifferentiation trajectory during postinjury lung regeneration, including previously unknown intermediate cell states, which we confirm experimentally.
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