B. J. Raphael

A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors

This paper introduces fastBE, a method for phylogenetic reconstruction from bulk DNA sequencing data that improves accuracy and scalability over existing approaches.

HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data

HATCHet2 improves copy number inference from bulk tumor sequencing by identifying clone- and haplotype-specific aberrations, revealing new mirrored-subclonal CNAs in prostate cancer.

Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

This study analyzes SCNAs in osteosarcoma using single-cell DNA sequencing, finding limited heterogeneity and suggesting early catastrophic events drive genomic complexity.

Integrating genetic dependencies and genomic alterations across pathways and cancer types

The paper introduces SuperDendrix to analyze genetic dependencies and genomic alterations across cancer cell lines, revealing pathway-specific associations and lineage-specific transcription factor dependencies.

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples

This paper introduces RCK, an algorithm to reconstruct clone- and haplotype-specific cancer karyotypes from bulk tumor samples, showing improved accuracy over existing methods.

A statistical test on single-cell data reveals widespread recurrent mutations in tumor evolution

This study tests the infinite sites assumption in tumor evolution using single-cell sequencing data and finds recurrent mutations in multiple datasets.