ArticleAlgorithms for molecular biology : AMB2017
Complexity and algorithms for copy-number evolution problems.
Article in Algorithms for molecular biology : AMB, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 47 citations in OpenAlex.
- Trial
- Single-cell copy number calling and event history reconstruction.Bioinformatics (Oxford, England) · 2025Article
- DICE: fast and accurate distance-based reconstruction of single-cell copy number phylogenies.Life science alliance · 2025Article
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- Inference of chromosome selection parameters and missegregation rate in cancer from DNA-sequencing data.Scientific reports · 2024Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.Genome biology · 2024Article
- A war on many fronts: cross disciplinary approaches for novel cancer treatment strategies.Frontiers in genetics · 2024Review
- A zero-agnostic model for copy number evolution in cancer.PLoS computational biology · 2023Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.bioRxiv : the preprint server for biology · 2023Article
- A zero-agnostic model for copy number evolution in cancer.bioRxiv : the preprint server for biology · 2023Article
- Article
- Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time.Cancer research communications · 2023Article
- Parsimonious Clone Tree Integration in cancer.Algorithms for molecular biology : AMB · 2022Article
- Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data.Bioinformatics (Oxford, England) · 2021Article
- MEDALT: single-cell copy number lineage tracing enabling gene discovery.Genome biology · 2021Article
- Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL.Nature biotechnology · 2021Article
- Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data.Nature communications · 2020Article
- Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data.PLoS computational biology · 2020Article
- Copy number evolution with weighted aberrations in cancer.Bioinformatics (Oxford, England) · 2020Article
- Phylogenetic reconstruction of breast cancer reveals two routes of metastatic dissemination associated with distinct clinical outcome.EBioMedicine · 2020Article
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundCancer is an evolutionary process characterized by the accumulation of somatic mutations in a population of cells that form a tumor. One frequent type of mutations is copy number aberrations, which alter the number of copies of genomic regions. The number of copies of each position along a chromosome constitutes the chromosome's copy-number profile. Understanding how such profiles evolve in cancer can assist in both diagnosis and prognosis.
resultsWe model the evolution of a tumor by segmental deletions and amplifications, and gauge distance from profile [Formula: see text] to [Formula: see text] by the minimum number of events needed to transform [Formula: see text] into [Formula: see text]. Given two profiles, our first problem aims to find a parental profile that minimizes the sum of distances to its children. Given
conclusionsFor the former problem we give a pseudo-polynomial dynamic programming algorithm that is linear in the profile length, and an integer linear program formulation. For the latter problem we show it is NP-hard and give an integer linear program formulation that scales to practical problem instance sizes. We assess the efficiency and quality of our algorithms on simulated instances. AVAILABILITY: https://github.com/raphael-group/CNT-ILP.
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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.