ArticleCell reports methods2022
Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision.
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 9 papers.
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Who cites it
9 citing papers in PubMed.
- 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
- Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis.Nature genetics · 2026Article
- Clinical Context Shapes the Relationship between Genomic Alterations and Response to AR Inhibitors and Chemotherapy in Metastatic Prostate Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Article
- Article
- Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution.Nature genetics · 2024Article
- Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN.Nature methods · 2024Article
- Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN.bioRxiv : the preprint server for biology · 2023Article
- Article
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Abstract
Recent advances in CRISPR-Cas9 engineering and single-cell assays have enabled the simultaneous measurement of single-cell transcriptomic and phylogenetic profiles. However, there are few computational tools enabling users to integrate and derive insight from a joint analysis of these two modalities. Here, we describe "PhyloVision": an open-source software for interactively exploring data from both modalities and for identifying and interpreting heritable gene modules whose concerted expression are associated with phylogenetic relationships. PhyloVision provides a feature-rich, interactive, and shareable web-based report for investigating these modules while also supporting several other data and meta-data exploration capabilities. We demonstrate the utility of PhyloVision using a published dataset of metastatic lung adenocarcinoma cells, whose phylogeny was resolved using a CRISPR-Cas9-based lineage-tracing system. Together, we anticipate that PhyloVision and the methods it implements will be a useful resource for scalable and intuitive data exploration for any assay that simultaneously measures cell state and lineage.
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