Machine Learning

Reconstructing the evolutionary history of tumors

clonal-no italics

Phylo* is a family of statistical methods that use nonparametric Bayesian tree priors to infer clonal evolution of tumors from whole genome sequencing data.

References

Amit G. Deshwar, Shankar Vembu, Christina K. Yung, Gun Ho Jang, Lincoln Stein, Quaid Morris. PhyloWGS: Reconstructing subclonal composition and evolution from whole genome sequencing of tumors. Genome Biology 16:35, 2015.

http://genomebiology.com/2015/16/1/35/abstract

https://github.com/morrislab/phylowgs

 

Amit G. Deshwar, Shankar Vembu, Quaid Morris. Comparing Nonparametric Bayesian Tree priors for clonal reconstruction of tumors. InProceedings of the Pacific Symposium on Biocomputing, 2015.

http://www.worldscientific.com/doi/abs/10.1142/9789814644730_0004

 

Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris. Inferring clonal Evolution of tumors from single nucleotide Somatic Mutations. BMC Bioinformatics 15:35, 2014.

http://www.biomedcentral.com/1471-2105/15/35

https://github.com/morrislab/phylosub