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References from Cancer phylogenetic tree inference at scale from 1000s of single cell genomes. Local targets link to admitted publications; unresolved targets remain external evidence.
Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution
10.1038/nature22364 · 2017 · External reference
Probability Distributions on Cladograms
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Genome-wide copy number analysis of single cells
10.1038/nprot.2012.039 · 2012 · External reference
Which Random Processes Describe the Tree of Life? A Large-Scale Study of Phylogenetic Tree Imbalance
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apTreeshape: statistical analysis of phylogenetic tree shape
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Blang: Bayesian Declarative Modeling of General Data Structures and Inference via Algorithms Based on Distribution Continua
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Density-Based Clustering Based on Hierarchical Density Estimates
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Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle
10.1089/106652702761034136 · 2002 · External reference
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution
10.1038/nature13952 · 2014 · External reference
Punctuated copy number evolution and clonal stasis in triple-negative breast cancer
10.1038/ng.3641 · 2016 · External reference
Single-cell genome sequencing: current state of the science
10.1038/nrg.2015.16 · 2016 · External reference
Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images
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Estimation of rearrangement phylogeny for cancer genomes
10.1101/gr.118414.110 · 2012 · External reference
Estimation of rearrangement phylogeny for cancer genomes
10.1101/gr.118414.110 · 2011 · External reference
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
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Phenotypic plasticity and genetic control in colorectal cancer evolution
10.1038/s41586-022-05311-x · 2022 · External reference
MRBAYES: Bayesian inference of phylogenetic trees
10.1093/bioinformatics/17.8.754 · 2001 · External reference
Tree inference for single-cell data
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MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
10.1186/s13059-022-02794-9 · 2022 · External reference
The coalescent
10.1016/0304-4149(82)90011-4 · 1982 · External reference
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
10.1093/oxfordjournals.molbev.a040126 · 1994 · External reference
Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing
10.1016/j.cell.2019.10.026 · 2019 · External reference
Phylogenetic reconstruction from copy number aberration in large scale, low-depth genome-wide single-cell data
10.24072/pci.mcb.100112 · 2023 · External reference
Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer
10.1101/gr.209973.116 · 2017 · External reference
On Sackin’s original proposal: the variance of the leaves’ depths as a phylogenetic balance index
10.1186/s12859-020-3405-1 · 2020 · External reference
The infinite sites model of genome evolution
10.1073/pnas.0805217105 · 2008 · External reference
Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data
10.1038/s41467-019-10737-5 · 2019 · External reference
Methods for copy number aberration detection from single-cell DNA-sequencing data
10.1186/s13059-020-02119-8 · 2020 · External reference
Clonal decomposition and DNA replication states defined by scaled single cell genome sequencing (Version v2) [Data set].
10.5281/zenodo.3445364 · 2019 · External reference
SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution
10.1371/journal.pcbi.1003665 · 2014 · External reference
Different Facets of Copy Number Changes: Permanent, Transient, and Adaptive
10.1128/mcb.00652-15 · 2016 · External reference
Slice sampling
10.1214/aos/1056562461 · 2003 · External reference
Genealogies of rapidly adapting populations
10.1073/pnas.1213113110 · 2012 · External reference
10.1007/978-1-4614-1743-9
10.1007/978-1-4614-1743-9 · 2012 · External reference
High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics
10.1101/gr.232272.117 · 2018 · External reference
Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts
10.1126/science.abc1944 · 2021 · External reference
Comparison of phylogenetic trees
10.1016/0025-5564(81)90043-2 · 1981 · External reference
OncoNEM: inferring tumor evolution from single-cell sequencing data
10.1186/s13059-016-0929-9 · 2016 · External reference
A Beta-splitting model for evolutionary trees
10.1098/rsos.160016 · 2016 · External reference
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
10.1093/oxfordjournals.molbev.a040454 · 1987 · External reference
UBC-Stat-ML/sitka_data: Sitka data publication (Dataset)
10.5281/zenodo.8051016 · 2023 · External reference
UBC-Stat-ML/sitkatree: Sitka publication (Code)
10.5281/zenodo.8050973 · 2023 · External reference
Clonal fitness inferred from time-series modelling of single-cell cancer genomes
10.1038/s41586-021-03648-3 · 2021 · External reference
SCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses
10.1016/j.cels.2020.04.001 · 2020 · External reference
phangorn: phylogenetic analysis in R
10.1093/bioinformatics/btq706 · 2010 · External reference
The evolution of tumour phylogenetics: principles and practice
10.1038/nrg.2016.170 · 2017 · External reference
SCIΦ: Single-cell mutation identification via phylogenetic inference
10.1101/290908 · External reference
A statistical method for evaluating systematic relationships.
1958 · External reference
ML or NJ-MCL? A comparison between two robust phylogenetic methods
10.1016/j.compbiolchem.2009.07.007 · 2009 · External reference
Coala: an R framework for coalescent simulation
10.1093/bioinformatics/btw098 · 2016 · External reference
Dirichlet Process
10.1007/978-0-387-30164-8_219 · 2011 · External reference
MEDALT: single-cell copy number lineage tracing enabling gene discovery
10.1186/s13059-021-02291-5 · 2021 · External reference
Clonal evolution in breast cancer revealed by single nucleus genome sequencing
10.1038/nature13600 · 2014 · External reference
An investigation of phylogenetic likelihood methods
10.1109/bibe.2003.1188932 · 2003 · External reference
Generating Random Spanning Trees More Quickly Than the Cover Time
10.1145/237814.237880 · 1996 · External reference
Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor
10.1016/j.cell.2012.02.025 · 2012 · External reference
Patterns and mechanisms of structural variations in human cancer
10.1038/s12276-018-0112-3 · 2018 · External reference
Index for rating diagnostic tests
10.1002/1097-0142(1950)3:1<32::aid-cncr2820030106>3.0.co;2-3 · 1950 · External reference
Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing
10.1038/cr.2014.43 · 2014 · External reference
SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models
10.1186/s13059-017-1311-2 · 2017 · External reference
Scalable whole-genome single-cell library preparation without preamplification
10.1038/nmeth.4140 · 2017 · External reference
