ArticleNature methods2020
Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.
Article in Nature methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 82 citations in OpenAlex.
- ST-LDAW: A Topic-Model and Damped Weighted Least-Squares Method for Integrative Deconvolution of Single-Cell and Spatial Transcriptomics.Interdisciplinary sciences, computational life sciences · 2026Article
- 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
- SNPmanifold: detecting single-cell clonality and lineages from single-nucleotide variants using binomial variational autoencoder.Genome biology · 2025Article
- Network based simultaneous embedding of cells and marker genes from scRNA-seq studies.Briefings in bioinformatics · 2025Article
- Temporal multi-omics analysis of COVID-19 in end-stage kidney disease.Cell genomics · 2025Article
- Single-cell genome and transcriptome sequencing without upfront whole-genome amplification reveals cell state plasticity of melanoma subclones.Nucleic acids research · 2025Article
- 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
- Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones.Cell systems · 2025Article
- 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
- Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.Nature communications · 2024Article
- Mimicking and analyzing the tumor microenvironment.Cell reports methods · 2024Review
- Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution.Nature communications · 2024Article
- De novo detection of somatic mutations in high-throughput single-cell profiling data sets.Nature biotechnology · 2024Article
- Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones.bioRxiv : the preprint server for biology · 2024Article
- Joint inference of clonal structure using single-cell genome and transcriptome sequencing data.NAR genomics and bioinformatics · 2024Article
- A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data.Genome research · 2024Article
- Accurate integration of single-cell DNA and RNA for analyzing intratumor heterogeneity using MaCroDNA.Nature communications · 2023Article
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Authors and funding
14 authors at 6 institutions in 5 countries.
Funding
Abstract
Bulk and single-cell DNA sequencing has enabled reconstructing clonal substructures of somatic tissues from frequency and cooccurrence patterns of somatic variants. However, approaches to characterize phenotypic variations between clones are not established. Here we present cardelino (https://github.com/single-cell-genetics/cardelino), a computational method for inferring the clonal tree configuration and the clone of origin of individual cells assayed using single-cell RNA-seq (scRNA-seq). Cardelino flexibly integrates information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. We apply cardelino to a published cancer dataset and to newly generated matched scRNA-seq and exome-seq data from 32 human dermal fibroblast lines, identifying hundreds of differentially expressed genes between cells from different somatic clones. These genes are frequently enriched for cell cycle and proliferation pathways, indicating a role for cell division genes in somatic evolution in healthy skin.
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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.