ArticleGenome biology2016
OncoNEM: inferring tumor evolution from single-cell sequencing data.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 145 papers.
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Who cites it
145 citing papers in PubMed.
- Phylogenetic and phylodynamic approaches to understanding the evolution of non-small cell lung cancer using single-cell sequencing.Oncogene · 2026Article
- Statistical Inconsistency of Error-correction Objectives for Perfect Phylogenies.bioRxiv : the preprint server for biology · 2026Article
- INHBA secreted by cancer-associated fibroblasts promotes cisplatin resistance and malignant progression of ovarian cancer via ENG-mediated suppression of apoptosis and induction of EMT.Journal of translational medicine · 2026Article
- Single-cell genomic analysis of cancer cells from one treatment-naïve patient with metastatic prostate cancer.BMC genomic data · 2026Article
- Single-cell omics data-driven decoding of tumor clonal evolution through reinforcement learning.Genome medicine · 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
- Discovery and validation of proliferative exhausted T cells as a favorable prognostic biomarker in esophageal squamous cell carcinoma.Scientific reports · 2025Article
- DelSIEVE: cell phylogeny modeling of single nucleotide variants and deletions from single-cell DNA sequencing data.Genome biology · 2025Article
- Review
- Single-Cell RNA Sequencing in Unraveling Acquired Resistance to EGFR-TKIs in Non-Small Cell Lung Cancer: New Perspectives.International journal of molecular sciences · 2025Review
- Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs.Bioinformatics advances · 2025Review
- HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures.PLoS computational biology · 2024Article
- TCfinder: Robust tumor cell discrimination in scRNA-seq based on gene pathway activity.iMetaOmics · 2024Article
- Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution.Nature communications · 2024Article
- Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.bioRxiv : the preprint server for biology · 2024Article
- Oncotree2vec - a method for embedding and clustering of tumor mutation trees.Bioinformatics (Oxford, England) · 2024Article
- Single-cell and spatial transcriptomics reveal a high glycolysis B cell and tumor-associated macrophages cluster correlated with poor prognosis and exhausted immune microenvironment in diffuse large B-cell lymphoma.Biomarker research · 2024Article
- Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples.Nature protocols · 2024Review
- Resolving tumor evolution: a phylogenetic approach.Journal of the National Cancer Center · 2024Review
85 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Single-cell sequencing promises a high-resolution view of genetic heterogeneity and clonal evolution in cancer. However, methods to infer tumor evolution from single-cell sequencing data lag behind methods developed for bulk-sequencing data. Here, we present OncoNEM, a probabilistic method for inferring intra-tumor evolutionary lineage trees from somatic single nucleotide variants of single cells. OncoNEM identifies homogeneous cellular subpopulations and infers their genotypes as well as a tree describing their evolutionary relationships. In simulation studies, we assess OncoNEM's robustness and benchmark its performance against competing methods. Finally, we show its applicability in case studies of muscle-invasive bladder cancer and essential thrombocythemia.
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