Author

B. J. Raphael

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Cancer Biology· 5

Signature Assays, Organisms & Methods

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Organism:human· 5 Approach:statistical model· 5 Research Focus:clustering· 3 Approach:deep learning· 3 Research Focus:variant calling· 3 Assay:whole-genome sequencing· 3 Research Focus:cancer & tumor microenvironment· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

S. Zaccaria· 2 shared A. C. Gross· 1 shared B. J. Arnold· 1 shared G. W. Klau· 1 shared J. Kuipers· 1 shared K. Jahn· 1 shared K. M. Mullen· 1 shared M. A. Myers· 1 shared

Activity by Year

2016-2023 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 11 mutual co-author links

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2 shared papersCancer Biology

S. Zaccaria

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Author profile →

5 papers

Recent·Most cited

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

M. A. Myers, B. J. Arnold, V. Bansal, K. M. Mullen, S. Zaccaria, B. J. Raphael

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

bioRxiv · Jul 13, 2023Cancer Biology

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

S. Rajan, S. Zaccaria, M. V. Cannon, M. Cam, A. C. Gross, B. J. Raphael, R. D. Roberts

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

bioRxiv · Aug 30, 2021Cancer Biology

Integrating genetic dependencies and genomic alterations across pathways and cancer types

T. Y. Park, M. D. M. Leiserson, G. W. Klau, B. J. Raphael

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.

bioRxiv · Jul 13, 2020Cancer Biology

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

S. Aganezov, B. J. Raphael

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

bioRxiv · Feb 25, 2019Cancer Biology

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

J. Kuipers, K. Jahn, B. J. Raphael, N. Beerenwinkel

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

bioRxiv · Dec 16, 2016Cancer Biology