Clonal reconstruction from time course genomic sequencing data

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data

MOTIVATION DNA sequencing of multiple samples from the same tumor provides data to analyze the process of clonal evolution in the population of cells that give rise to a tumor. RESULTS We formalize the problem of reconstructing the clonal evolution of a tumor using single-nucleotide mutations as the variant allele frequency (VAF) factorization problem. We derive a combinatorial characterizati...

Image Reconstruction from Incomplete Data

Genotype Calling from Population-Genomic Sequencing Data

Genotype calling plays important roles in population-genomic studies, which have been greatly accelerated by sequencing technologies. To take full advantage of the resultant information, we have developed maximum-likelihood (ML) methods for calling genotypes from high-throughput sequencing data. As the statistical uncertainties associated with sequencing data depend on depths of coverage, we ha...

Image Reconstruction from Incomplete Data

Phylogenetic reconstruction from non-genomic data

MOTIVATION Recent results related to horizontal gene transfer suggest that phylogenetic reconstruction cannot be determined conclusively from sequence data, resulting in a shift from approaches based on polymorphism information in DNA or protein sequence to studies aimed at understanding the evolution of complete biological processes. The increasing amount of available information on metabolic ...