ArticleNature methods2024
CellRank 2: unified fate mapping in multiview single-cell data.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 149 papers.
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Who cites it
149 citing papers in PubMed.
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- Cell-level random splits leak group-owned answers in single-cell benchmarks.bioRxiv : the preprint server for biology · 2026Article
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- Plasticity of human microglia and brain perivascular macrophages in aging and Alzheimer's disease.Nature genetics · 2026Article
- Longitudinal alignments and syntheses of multimodal clinical data for personalized medicine with the PULSE framework.Nature computational science · 2026Article
- DEAPLOG: Differential Expression Analysis and Pseudo-Temporal Locating and Ordering of Genes in Single-Cell Transcriptomic Data.Interdisciplinary sciences, computational life sciences · 2026Article
- mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.Bioinformatics (Oxford, England) · 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
- Transposable elements and homotypic niches drive immune dynamics and resistance in melanoma epigenetic-based immunotherapy.Science advances · 2026Article
- Global StationaryOT: trajectory inference for aging time courses of single-cell snapshots.Bioinformatics (Oxford, England) · 2026Article
- Myofibroblastic CAF and Malignant Ductal Cell Crosstalk Drives Epithelial-Mesenchymal Transition and Progression in Pancreatic Ductal Adenocarcinoma via THBS2-SDC/Integrin Axes.International journal of molecular sciences · 2026Article
- RUNX2 promotes chromatin accessibility and WNT signaling in inflamed intestinal epithelial cells.Mucosal immunology · 2026Article
- Single-Cell Virtual Perturbation Screening Identifies STAT3 as a Key Regulator of Dentinogenesis.Cell proliferation · 2026Article
- SKIM: A fast sketching strategy integrated with model's dynamic-feedback for large-scale single-cell transcriptomic analysis.PLoS computational biology · 2026Article
89 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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Abstract
Single-cell RNA sequencing allows us to model cellular state dynamics and fate decisions using expression similarity or RNA velocity to reconstruct state-change trajectories; however, trajectory inference does not incorporate valuable time point information or utilize additional modalities, whereas methods that address these different data views cannot be combined or do not scale. Here we present CellRank 2, a versatile and scalable framework to study cellular fate using multiview single-cell data of up to millions of cells in a unified fashion. CellRank 2 consistently recovers terminal states and fate probabilities across data modalities in human hematopoiesis and endodermal development. Our framework also allows combining transitions within and across experimental time points, a feature we use to recover genes promoting medullary thymic epithelial cell formation during pharyngeal endoderm development. Moreover, we enable estimating cell-specific transcription and degradation rates from metabolic-labeling data, which we apply to an intestinal organoid system to delineate differentiation trajectories and pinpoint regulatory strategies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.