ArticleProceedings of the National Academy of Sciences of the United States of America2008
The infinite sites model of genome evolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Agent-Based Simulations of Lung Tumor Evolution Suggest That Ongoing Cell Competition Drives Realistic Clonal Expansions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Statistical Inconsistency of Error-correction Objectives for Perfect Phylogenies.bioRxiv : the preprint server for biology · 2026Article
- A breakage-replication/fusion process explains complex rearrangements and segmental DNA amplification.Nature genetics · 2026Article
- Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them.Seminars in cell & developmental biology · 2025Review
- Estimating between-country migration in pneumococcal populations.G3 (Bethesda, Md.) · 2024Article
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- Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models.Genome research · 2023Article
- The role of APOBEC3-induced mutations in the differential evolution of monkeypox virus.Virus evolution · 2023Article
- Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors.Bioinformatics (Oxford, England) · 2022Article
- Estimating Genetic Similarity Matrices Using Phylogenies.Journal of computational biology : a journal of computational molecular cell biology · 2021Article
- Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples.Genome research · 2020Article
- Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Toward Recovering Allele-specific Cancer Genome Graphs.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Genetic alterations driving metastatic colony formation are acquired outside of the primary tumour in melanoma.Nature communications · 2018Article
- SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models.Genome biology · 2017Article
- Reconstructing metastatic seeding patterns of human cancers.Nature communications · 2017Article
- Article
- Isometric gene tree reconciliation revisited.Algorithms for molecular biology : AMB · 2017Article
- Article
- A unifying model of genome evolution under parsimony.BMC bioinformatics · 2014Article
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6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We formalize the problem of recovering the evolutionary history of a set of genomes that are related to an unseen common ancestor genome by operations of speciation, deletion, insertion, duplication, and rearrangement of segments of bases. The problem is examined in the limit as the number of bases in each genome goes to infinity. In this limit, the chromosomes are represented by continuous circles or line segments. For such an infinite-sites model, we present a polynomial-time algorithm to find the most parsimonious evolutionary history of any set of related present-day genomes.
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