ArticleCell stem cell2022
Capybara: A computational tool to measure cell identity and fate transitions.
Article in Cell stem cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Article
- Peritoneal ovarian cancer growth in the omentum proceeds independently of mature adipocytes.Nature communications · 2026Article
- MLL3 and MLL4 sustain hematopoietic stem cell multipotency by opposing a B-cell default state.Blood · 2026Article
- Transcriptional landscape of direct reprogramming toward the hematopoietic lineage.bioRxiv : the preprint server for biology · 2026Article
- Integrated single-cell transcriptomic analysis identifiesBiochemistry and biophysics reports · 2026Article
- Oscillatory co-expression of HES1 and HES5 enables a hybrid state in a cross-repressive transcription factor regulatory motif.Development (Cambridge, England) · 2026Article
- RECOMBINE identifies recurrent composite markers of cell types and states.Genome research · 2026Article
- Redefining cellular reprogramming with advanced genomic technologies.Nature reviews. Genetics · 2026Review
- Programmable nanobody circuits for cell selection.bioRxiv : the preprint server for biology · 2026Article
- scChat: A Large Language Model-Powered Co-Pilot for Contextualized Single-Cell RNA Sequencing Analysis.AIChE journal. American Institute of Chemical Engineers · 2026Article
- Fetal context conveys heritable protection against MLL-rearranged AML that depends on MLL3.Blood · 2026Article
- A novel paradigm for single-cell annotation in stem cell research.Stem cell reports · 2025Review
- Perspectives on integrating artificial intelligence and single-cell omics for cellular plasticity research.Quantitative biology (Beijing, China) · 2025Article
- Nicheformer: a foundation model for single-cell and spatial omics.Nature methods · 2025Article
- Dual SMAD inhibition as a versatile platform in human pluripotent stem cell-based regenerative medicine and disease modeling.Molecules and cells · 2025Review
- A unified multimodal single-cell framework reveals a discrete state model of hematopoiesis in mice.Nature immunology · 2025Article
- LogicSR: prior-guided symbolic regression for gene regulatory network inference from single-cell transcriptomics data.Briefings in bioinformatics · 2025Article
- Adipocytes are dispensable in shaping the ovarian cancer tumor microenvironment in the omentum.bioRxiv : the preprint server for biology · 2025Article
- CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data.Bioinformatics (Oxford, England) · 2025Article
- Cell and tissue reprogramming: Unlocking a new era in medical drug discovery.Pharmacological reviews · 2025Review
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7 authors.
Funding
Abstract
Measuring cell identity in development, disease, and reprogramming is challenging as cell types and states are in continual transition. Here, we present Capybara, a computational tool to classify discrete cell identity and intermediate "hybrid" cell states, supporting a metric to quantify cell fate transition dynamics. We validate hybrid cells using experimental lineage tracing data to demonstrate the multi-lineage potential of these intermediate cell states. We apply Capybara to diagnose shortcomings in several cell engineering protocols, identifying hybrid states in cardiac reprogramming and off-target identities in motor neuron programming, which we alleviate by adding exogenous signaling factors. Further, we establish a putative in vivo correlate for induced endoderm progenitors. Together, these results showcase the utility of Capybara to dissect cell identity and fate transitions, prioritizing interventions to enhance the efficiency and fidelity of stem cell engineering.
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Registered trials
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.