ArticleGenome biology2015
BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 147 citations in OpenAlex.
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- Cancer subclone detection based on DNA copy number in single-cell and spatial omic sequencing data.Nature methods · 2025Article
- DelSIEVE: cell phylogeny modeling of single nucleotide variants and deletions from single-cell DNA sequencing data.Genome biology · 2025Article
- Single-cell copy number calling and event history reconstruction.Bioinformatics (Oxford, England) · 2025Article
- SpatialSNV: A novel method for identifying and analyzing spatially resolved SNVs in tumor microenvironments.GigaScience · 2025Article
- Scuphr: A probabilistic framework for cell lineage tree reconstruction.PLoS computational biology · 2024Article
- Phylogenetic inference from single-cell RNA-seq data.Scientific reports · 2023Article
- Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data.Journal of computational biology : a journal of computational molecular cell biology · 2023Article
- Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.Nature communications · 2023Article
- RobustTree: An adaptive, robust PCA algorithm for embedded tree structure recovery from single-cell sequencing data.Frontiers in genetics · 2023Article
- SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data.Genome biology · 2022Article
- Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm.PLoS computational biology · 2022Article
- Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations.Bioinformatics (Oxford, England) · 2022Article
- SCSilicon: a tool for synthetic single-cell DNA sequencing data generation.BMC genomics · 2022Article
- Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data.Bioinformatics (Oxford, England) · 2021Article
- DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution.Cell systems · 2021Article
- PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity.BMC bioinformatics · 2021Article
- Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses.Bioinformatics (Oxford, England) · 2021Article
- Triplet-based similarity score for fully multilabeled trees with poly-occurring labels.Bioinformatics (Oxford, England) · 2021Article
- A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data.Bioinformatics (Oxford, England) · 2021Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 4 institutions in 2 countries.
Funding
Abstract
Cancer has long been understood as a somatic evolutionary process, but many details of tumor progression remain elusive. Here, we present BitPhylogenyBitPhylogeny, a probabilistic framework to reconstruct intra-tumor evolutionary pathways. Using a full Bayesian approach, we jointly estimate the number and composition of clones in the sample as well as the most likely tree connecting them. We validate our approach in the controlled setting of a simulation study and compare it against several competing methods. In two case studies, we demonstrate how BitPhylogeny BitPhylogeny reconstructs tumor phylogenies from methylation patterns in colon cancer and from single-cell exomes in myeloproliferative neoplasm.
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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.