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References from Improving cellular phylogenies through the integrated use of mutation order and optimality principles. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1056/nejmoa1113205
10.1056/nejmoa1113205 · External reference
10.1016/j.cell.2012.04.023
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10.1126/science.1253462 · External reference
10.1073/pnas.1525677113
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A phylogenetic approach to study the evolution of somatic mutational processes in cancer
10.1038/s42003-022-03560-0 · 2022 · External reference
Somatic evolutionary timings of driver mutations
10.1186/s12885-017-3977-y · 2018 · External reference
Clone phylogenetics reveals metastatic tumor migrations, maps, and models
2022 · External reference
MOCA for integrated analysis of gene expression and genetic variation in single cells
10.3389/fgene.2022.831040 · 2022 · External reference
Rapid evolution and biogeographic spread in a colorectal cancer
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Tracking cancer evolution reveals constrained routes to metastases: TRACERx renal
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Cancer genomics: one cell at a time
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Tree inference for single-cell data
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10.1093/bioinformatics/btaa172
10.1093/bioinformatics/btaa172 · External reference
CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data
10.1186/s13059-021-02583-w · 2022 · External reference
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity
10.1093/bioinformatics/btac186 · 2022 · External reference
A new method of inference of ancestral nucleotide and amino acid sequences
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10.1093/molbev/msab118 · External reference
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10.1101/gr.209973.116 · External reference
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10.1038/nmeth.3867 · External reference
10.1093/bioinformatics/bts507
10.1093/bioinformatics/bts507 · External reference
Bootstrap confidence for tumor evolution estimates from bulk sequencing data
2023 · External reference
phangorn: phylogenetic analysis in R
10.1093/bioinformatics/btq706 · 2010 · External reference
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
10.1038/ng.3573 · 2016 · External reference
Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution
10.1016/j.cell.2022.04.015 · 2022 · External reference
PathFinder: bayesian inference of clone migration histories in cancer
10.1093/bioinformatics/btaa795 · 2020 · External reference
10.1126/science.abc1944
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Migrations of cancer cells through the lens of phylogenetic biogeography
10.1038/s41598-021-96215-9 · 2021 · External reference
Delineation of tumor migration paths by using a bayesian biogeographic approach
2019 · External reference