The evolution of tumour phylogenetics: principles and practice
Rapid advances in high-throughput sequencing and a growing realization of the importance
of evolutionary theory to cancer genomics have led to a proliferation of phylogenetic studies …
of evolutionary theory to cancer genomics have led to a proliferation of phylogenetic studies …
A picture guide to cancer progression and monotonic accumulation models: evolutionary assumptions, plausible interpretations, and alternative uses
Cancer progression and monotonic accumulation models were developed to discover
dependencies in the irreversible acquisition of binary traits from cross-sectional data. They …
dependencies in the irreversible acquisition of binary traits from cross-sectional data. They …
Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics
SA Chowdhury, SE Shackney… - PLoS computational …, 2014 - journals.plos.org
We present methods to construct phylogenetic models of tumor progression at the cellular
level that include copy number changes at the scale of single genes, entire chromosomes …
level that include copy number changes at the scale of single genes, entire chromosomes …
Evolutionary accumulation modelling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance
Can we understand and predict the evolutionary pathways by which bacteria acquire multi-
drug resistance (MDR)? These questions have substantial potential impact in basic biology …
drug resistance (MDR)? These questions have substantial potential impact in basic biology …
Efficient sampling for Bayesian inference of conjunctive Bayesian networks
Motivation: Cancer development is driven by the accumulation of advantageous mutations
and subsequent clonal expansion of cells harbouring these mutations, but the order in which …
and subsequent clonal expansion of cells harbouring these mutations, but the order in which …
Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling
R Diaz-Uriarte - BMC bioinformatics, 2015 - Springer
Background Cancer progression is caused by the sequential accumulation of mutations, but
not all orders of accumulation are equally likely. When the fixation of some mutations …
not all orders of accumulation are equally likely. When the fixation of some mutations …
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
In genetics, many evolutionary pathways can be modeled by the ordered accumulation of
permanent changes. Mixture models of mutagenetic trees have been used to describe …
permanent changes. Mixture models of mutagenetic trees have been used to describe …
Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV
Background Disease progression models are important for understanding the critical steps
during the development of diseases. The models are imbedded in a statistical framework to …
during the development of diseases. The models are imbedded in a statistical framework to …
[PDF][PDF] Sample Size Estimation for Cancer Progression Models
C Netzer, J Rahnenführer - International Journal of Computational …, 2012 - Citeseer
Human tumours are often associated with the accumulation of chromosomal alterations in
the cancer cells. The identification of characteristic pathogenic routes improves prediction of …
the cancer cells. The identification of characteristic pathogenic routes improves prediction of …
Inferring restrictions in the temporal order of mutations during tumor progression: effects of passenger mutations, evolutionary models, and sampling
R Diaz-Uriarte - bioRxiv, 2014 - biorxiv.org
Cancer progression is caused by the sequential accumulation of mutations, but not all
orders of accumulation of mutations are equally likely. When the fixation of some mutations …
orders of accumulation of mutations are equally likely. When the fixation of some mutations …