Character-based phylogeny construction and its application to tumor evolution

DOI10.1007/978-3-319-58741-7_1MaRDI QIDQ2011627zbMATH OpenOpenAlexFDO

Authors Gianluca Della Vedova, Murray Patterson, Raffaella Rizzi, Mauricio Soto

Publication date 4 August 2017

Full work available at URL https://doi.org/10.1007/978-3-319-58741-7_1

Mathematics Subject Classification ID

Applications of graph theory (05C90) Problems related to evolution (92D15)

Recommendations

• Combinatorial Pattern Matching
• Algorithms for phylogeny reconstruction in a new mathematical model
• Reconstructing mutational history in multiply sampled tumors using perfect phylogeny mixtures
• Finding a perfect phylogeny from mixed tumor samples
• scientific article; zbMATH DE number 1303534

Cites work

• A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies
• A Polynomial-Time Algorithm For the Perfect Phylogeny Problem When the Number of Character States is Fixed
• A colored graph approach to perfect phylogeny with persistent characters
• A linear-time algorithm for the perfect phylogeny haplotype problem
• Algorithms on Strings, Trees and Sequences
• Efficient algorithms for inferring evolutionary trees
• Haplotyping with missing data via perfect path phylogenies
• Incomplete Directed Perfect Phylogeny
• Minimizing phylogenetic number to find good evolutionary trees
• On the Generalised Character Compatibility Problem for Non-branching Character Trees
• Phylogeny. Discrete and random processes in evolution
• Research in Computational Molecular Biology
• Research in Computational Molecular Biology
• Testing for the consecutive ones property, interval graphs, and graph planarity using PQ-tree algorithms
• The binary perfect phylogeny with persistent characters

Cited in

(5)

• Reconstructing mutational history in multiply sampled tumors using perfect phylogeny mixtures
• Phyolin: identifying a linear perfect phylogeny in single-cell DNA sequencing data of tumors
• Inferring temporally consistent migration histories
• Finding a perfect phylogeny from mixed tumor samples
• Copy-number evolution problems: complexity and algorithms

Describes a project that uses

Uses Software

• SPRUCE
• AncesTree
• rec-BTP
• PyClone
• SNV-PPILP

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