ArticleCell genomics2023
ClonoCluster: A method for using clonal origin to inform transcriptome clustering.
Article in Cell genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 20 citations in OpenAlex.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- A single-cell lens into the co-evolution of genotypes and phenotypes in cancer.Nature reviews. Cancer · 2026Review
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data.bioRxiv : the preprint server for biology · 2026Article
- Single-cell lineage tracing maps clonal and transcriptional dynamics in melanoma metastasis.bioRxiv : the preprint server for biology · 2026Article
- Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance.Molecular cancer · 2026Article
- Integrating synthetic biology to understand and engineer the heart, lung, blood, and sleep systems.Cell systems · 2025Review
- Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance.bioRxiv : the preprint server for biology · 2025Article
- Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer.NPJ systems biology and applications · 2025Article
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- Single-Cell Lineage Tracing and Clonal State-Fate Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets.Nature communications · 2024Article
- Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells.Cell systems · 2024Article
- Craniofacial developmental biology in the single-cell era.Development (Cambridge, England) · 2023Review
- Article
- Toward a systems-level probing of tumor clonality.iScience · 2023Review
- Article
- Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells.bioRxiv : the preprint server for biology · 2023Article
- Integration of quantitative methods and mathematical approaches for the modeling of cancer cell proliferation dynamics.American journal of physiology. Cell physiology · 2023Review
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Clustering cells based on their high-dimensional profiles is an important data reduction process by which researchers infer distinct cellular states. The advent of cellular barcoding, however, provides an alternative means by which to group cells: by their clonal origin. We developed ClonoCluster, a computational method that combines both clone and transcriptome information to create hybrid clusters that weight both kinds of data with a tunable parameter. We generated hybrid clusters across six independent datasets and found that ClonoCluster generated qualitatively different clusters in all cases. The markers of these hybrid clusters were different but had equivalent fidelity to transcriptome-only clusters. The genes most strongly associated with the rearrangements in hybrid clusters were ribosomal function and extracellular matrix genes. We also developed the complementary tool Warp Factor that incorporates clone information in popular 2D visualization techniques like UMAP. Integrating ClonoCluster and Warp Factor revealed biologically relevant markers of cell identity.
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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.