ArticleNature communications2023
Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Phylogenetic tree inference from single-cell RNA sequencing data with SCITE-RNA.Genome biology · 2026Article
- DAESC + : high-performance, integrated software for single-cell allele-specific expression data.BMC bioinformatics · 2026Article
- Interpreting cancer genetics through a two-step "evolutionary cascade hypothesis": bridging neutral and selective perspectives.Journal of translational medicine · 2026Review
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- De Novo Detection of Clonal Structure and Evolution in Single-Cell and Spatial Transcriptomes.International journal of molecular sciences · 2025Article
- Precision Oncology: Current Landscape, Emerging Trends, Challenges, and Future Perspectives.Cells · 2025Review
- Integration of multi-omics approaches in exploring intra-tumoral heterogeneity.Cancer cell international · 2025Review
- Deconvolution and Phylogeny Inference of Diverse Variant Types Integrating Bulk DNA-seq with Single-cell RNA-seq.bioRxiv : the preprint server for biology · 2025Article
- ScLineageAtlas: a comprehensive single-cell genomics database for characterizing cellular clones in cancer.Database : the journal of biological databases and curation · 2025Article
- Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs.Bioinformatics advances · 2025Review
- Deconvolution and phylogeny inference of diverse variant types integrating bulk DNA-seq with single-cell RNA-seq.Bioinformatics advances · 2025Article
- CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants.Genome biology · 2024Article
- Computational methods for allele-specific expression in single cells.Trends in genetics : TIG · 2024Review
- Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.Nature communications · 2024Article
- CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics.Bioinformatics (Oxford, England) · 2024Article
- Scuphr: A probabilistic framework for cell lineage tree reconstruction.PLoS computational biology · 2024Article
- A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data.Genome research · 2024Article
- Phylogenetic inference from single-cell RNA-seq data.Scientific reports · 2023Article
Corrections and comments
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12 authors.
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Abstract
Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer's proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer.
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